Browsing by Author "Nunez-Garcia J."

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    Corrigendum: Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens (Frontiers in Microbiology, (2023), 14, (1166615), 10.3389/fmicb.2023.1166615)
    (2023-01-01) Lopez-Garcia A.V.; AbuOun M.; Nunez-Garcia J.; Nale J.Y.; Gaylov E.E.; Phothaworn P.; Sukjoi C.; Thiennimitr P.; Malik D.J.; Korbsrisate S.; Clokie M.R.J.; Anjum M.F.; Mahidol University
    In the published article, there was an error in the Figure 3 and its legend as published. Figure 3B was removed from the manuscript; however, the associated legend text still needs to be removed and the key was not completely included in the original picture. The corrected Figure 3 and its caption appear below. Percentages of UK and Thai MDR, non-MDR, and sensitive isolates harboring virulence determinants. MDR isolates from the UK (green), non-MDR isolates from the UK (grey), sensitive isolates from the UK (blue), MDR isolates from Thailand (pink), non-MDR isolates from Thailand (yellow), and sensitive isolates from Thailand (orange) have been included. In the published article, there was an error in Table 1 as published. strA, strB and tetA(B) genes were misspelt as straA, straB and tet-AB. The corrected Table 1 and its caption appear below. AMR genotypes of 143 isolates identified by the APHA Seqfinder. AMR genes were grouped according to antimicrobial classes, and they are shown alongside the percentage of isolates per country harboring the AMR gene. In the published article, the reference for the virulence genes safBCD, srfJ, lpfD, and fhuA were present in both MDR S. Kentucky isolates, which were identified as clones of a ST198 S. Kentucky global lineage (Martínez and Baquero, 2002; Beceiro et al., 2013) was incorrectly written as (Martínez and Baquero, 2002; Beceiro et al., 2013). It should be deleted. In the published article, there was an error to Materials and methods, Phylogenetic and SNP analysis. The reference name should not contain commas. This sentence previously stated: “Snippy version v4.6.0 (Seemann, 2015) was used to detect SNPs in the core genome of S. Kentucky isolates BL700 and BL800, and two S. Kentucky MDR ST198 isolates from earlier research [SAMN08784244 and SAMN08784253; (Hawkey et al., 2019)], aligning them against the reference 201,001,922 (CP028357).” The corrected sentence appears below: “Snippy version v4.6.0 (Seemann, 2015) was used to detect SNPs in the core genome of S. Kentucky isolates BL700 and BL800, and two S. Kentucky MDR ST198 isolates from earlier research [SAMN08784244 and SAMN08784253; (Hawkey et al., 2019)], aligning them against the reference 201001922 (CP028357).” In the published article, there was an error in Results, Antimicrobial resistance characterization. The Thai S.1,4,12:i:- isolate does not present resistance to streptomycin. This sentence previously stated: “One Thai isolate, serotyped as S. 1,4,12:i:-, was resistant to seven antimicrobial classes (ampicillin, chloramphenicol, ciprofloxacin-nalidixic acid, gentamicin-streptomycin, sulfamethoxazole, tetracycline, and trimethoprim).” The corrected sentence appears below: “One Thai isolate, serotyped as S. 1,4,12:i:-, was resistant to seven antimicrobial classes (ampicillin, chloramphenicol, ciprofloxacin-nalidixic acid, gentamicin, sulfamethoxazole, tetracycline, and trimethoprim).” In the published article, there was an error in Results, Characterization of MDR isolates with distinct virulence profiles, 3rd Paragraph. The tetA(B) gene was misspelt. This sentence previously stated: “From the resolved genome of MDR isolate BL708 S. 1,4,[5],12:i:-, we identified SGI-4 in the chromosome with genes showing resistance to copper, arsenic, mercury, and antimicrobials [blaTem−1b, sul2, tet(AB), strA, strB].” The corrected sentence appears below: “From the resolved genome of MDR isolate BL708 S. 1,4,[5],12:i:-, we identified SGI-4 in the chromosome with genes showing resistance to copper, arsenic, mercury, and antimicrobials [blaTEM−1B, sul2, tetA(B), strA, strB].” In the published article, there was an error with the percentage of MDR isolates reported in the Author's Summary. The sentence previously stated: “The results indicated genes harboring resistance to antimicrobials differed between the countries, possibly due to differing farming practices; however, 17–18% of all isolates were multidrug resistant.” The corrected sentence appears below: “The results indicated genes harboring resistance to antimicrobials differed between the countries, possibly due to differing farming practices; however, 14%−15% of all isolates were multidrug resistant.” In the published article, there was an error in Supplementary Table S5. The tet-AB gene was misspelt and should be replaced by tetA(B). The supplementary table with the error typo amended has been submitted. The authors apologize for these errors and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.
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    Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens
    (2023-01-01) Lopez-Garcia A.V.; AbuOun M.; Nunez-Garcia J.; Nale J.Y.; Gaylov E.E.; Phothaworn P.; Sukjoi C.; Thiennimitr P.; Malik D.J.; Korbsrisate S.; Clokie M.R.J.; Anjum M.F.; Mahidol University
    Salmonella is a food-borne pathogen often linked to poultry sources, causing gastrointestinal infections in humans, with the numbers of multidrug resistant (MDR) isolates increasing globally. To gain insight into the genomic diversity of common serovars and their potential contribution to disease, we characterized antimicrobial resistance genes, and virulence factors encoded in 88 UK and 55 Thai isolates from poultry; the presence of virulence genes was detected through an extensive virulence determinants database compiled in this study. Long-read sequencing of three MDR isolates, each from a different serovar, was used to explore the links between virulence and resistance. To augment current control methods, we determined the sensitivity of isolates to 22 previously characterized Salmonella bacteriophages. Of the 17 serovars included, Salmonella Typhimurium and its monophasic variants were the most common, followed by S. Enteritidis, S. Mbandaka, and S. Virchow. Phylogenetic analysis of Typhumurium and monophasic variants showed poultry isolates were generally distinct from pigs. Resistance to sulfamethoxazole and ciprofloxacin was highest in isolates from the UK and Thailand, respectively, with 14–15% of all isolates being MDR. We noted that >90% of MDR isolates were likely to carry virulence genes as diverse as the srjF, lpfD, fhuA, and stc operons. Long-read sequencing revealed the presence of global epidemic MDR clones in our dataset, indicating they are possibly widespread in poultry. The clones included MDR ST198 S. Kentucky, harboring a Salmonella Genomic Island-1 (SGI)-K, European ST34 S. 1,4,[5],12:i:-, harboring SGI-4 and mercury-resistance genes, and a S. 1,4,12:i:- isolate from the Spanish clone harboring an MDR-plasmid. Testing of all isolates against a panel of bacteriophages showed variable sensitivity to phages, with STW-77 found to be the most effective. STW-77 lysed 37.76% of the isolates, including serovars important for human clinical infections: S. Enteritidis (80.95%), S. Typhimurium (66.67%), S. 1,4,[5],12:i:- (83.3%), and S. 1,4,12: i:- (71.43%). Therefore, our study revealed that combining genomics and phage sensitivity assays is promising for accurately identifying and providing biocontrols for Salmonella to prevent its dissemination in poultry flocks and through the food chain to cause infections in humans.