Correction: Oniciuc, E. A.; et al. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes 2018, 9, 268.

Elena A. Oniciuc; Eleni Likotrafiti; Adrián Alvarez-Molina; Miguel Prieto; Jesús A. Santos; Avelino Alvarez-Ordóñez

doi:10.3390/genes9070315

,

and

¹

Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati 800008, Romania

²

Laboratory of Food Microbiology, Department of Food Technology, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki T.K. 57400, Greece

³

Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain

^*

Author to whom correspondence should be addressed.

Genes2018, 9(7), 315;https://doi.org/10.3390/genes9070315

This article belongs to the Special Issue Genetics and Genomics of Foodborne Pathogens

Version Notes

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The authors wish to make the following changes to their paper [1]. Due to an undetected mistake in the references management, certain errors appeared in the reference list and a reference was duplicated in Table 1. Consequently, three references have been changed as follows:

Table 1. Main research studies published in recent years applying whole genome sequencing (WGS) to characterize antimicrobial resistance (AMR) in foodborne bacteria.

Reference [51] “51. Kumar, N.; Mariappan, V.; Baddam, R.; Lankapalli, A.K.; Shaik, S.; Goh, K.L.; Loke, M.F.; Perkins, T.; Benghezal, M.; Hasnain, S.E.; et al. Comparative Genomic Analysis of Helicobacter pylori from Malaysia Identifies Three Distinct Lineages Suggestive of Differential Evolution. Nucleic Acids Res. 2015, 43, 324–335.” has been replaced by: “51. Qumar, S.; Majid, M.; Kumar, N.; Tiwari, S.K.; Semmler, T.; Devi, S.; Baddam, R.; Hussain, A.; Shaik, S.; Ahmed, N. Genome Dynamics and Molecular Infection Epidemiology of Multidrug-Resistant Helicobacter pullorum Isolates Obtained from Broiler and Free-Range Chickens in India. Appl. Environ. Microbiol. 2017, 83, e02305-16.”

Reference [44] “44. Rehman, M.U.; Zhang, H.; Iqbal, M.K.; Mehmood, K.; Huang, S.; Nabi, F.; Luo, H.; Lan, Y.; Li, J. Antibiotic Resistance, Serogroups, Virulence Genes, and Phylogenetic Groups of Escherichia coli Isolated from Yaks with Diarrhea in Qinghai Plateau, China. Gut Pathog. 2017, 9, 1–11.” has been replaced by “44. Rehman, M.A.; Yin, X.; Lepp, D.; Laing, C.; Ziebell, K.; Talbot, G.; Topp, E.; Diarra, M.S. Genomic Analysis of Third Generation Cephalosporin Resistant Escherichia coli from Dairy Cow Manure. Vet. Sci. 2017, 4, 4, doi:10.3390/vetsci4040057.”

Reference [60] “60. Wang, W.; Baloch, Z.; Peng, Z.; Hu, Y.; Xu, J.; Fanning, S.; Li, F. Genomic Characterization of a Large Plasmid Containing a bla_NDM-1 Gene Carried on Salmonella enterica Serovar Indiana C629 Isolate from China. BMC Infect. Dis. 2017, 17, 1–8.” has been replaced by “60. Wang, J.; Li, X.; Li, J.; Hurley, D.; Bai, X.; Yu, Z.; Cao, Y.; Wall, E.; Fanning, S.; Bai, L. Complete Genetic Analysis of a Salmonella enterica serovar Indiana Isolate Accompanying Four Plasmids Carrying mcr-1, ESBL and Other Resistance Genes in China. Vet. Microbiol. 2017, 210, 142–146, doi:10.1016/j.vetmic.2017.08.024.”

Two references have been added, as they were omitted in error:

Reference [66] in Table 1 was wrongly cited, therefore it has been substituted by the new reference [66] “66. Li, B.; Yang, X.; Tan, H.; Ke, B.; He, D.; Wang, H.; Chen, Q.; Ke, C.; Zhang, Y. Whole Genome Sequencing Analysis of Salmonella enterica Serovar Weltevreden Isolated from Human Stool and Contaminated Food Samples Collected from the Southern Coastal Area of China. Int. J. Food Microbiol. 2018, 266, 317–323, doi:10.1016/j.ijfoodmicro.2017.10.032.”

Reference [8] in Table 1 was wrongly cited, therefore it has been substituted by the new reference [71] “71. Flórez, A.B.; Mayo, B. Antibiotic Resistance-Susceptibility Profiles of Streptococcus thermophilus Isolated from Raw Milk and Genome Analysis of the Genetic Basis of Acquired Resistances. Front. Microbiol. 2017, 8, 2608, doi:10.3389/fmicb.2017.02608.”

Due to this correction, reference numbers were adjusted to follow a numerical order. In [1], the previous references [66] and [71] are now [139] and [72], respectively.

The 31st row from Table 1, about S. enterica with origin in Dairy cattle and humans, was eliminated because it was a duplicate of row 28; the corrected table is:

The authors would like to apologize for any inconvenience caused to the readers by these changes.

References

Oniciuc, E.A.; Likotrafiti, E.; Alvarez-Molina, A.; Prieto, M.; Santos, J.A.; Alvarez-Ordóñez, A. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes 2018, 9, 268. [Google Scholar] [CrossRef] [PubMed]

Table 1. Main research studies published in recent years applying whole genome sequencing (WGS) to characterize antimicrobial resistance (AMR) in foodborne bacteria.

Reference	Microbial Species	Number of Isolates Sequenced	Origin	Main Findings in Relation to AMR
[36]	Aeromonas salmonicida	101	Fish	All sequenced isolates harbored three AMR genes against beta-lactam antibiotics encoded on the chromosome. Some isolates also harbored several other plasmid encoded resistance genes against trimethoprim, sulphonamide, and aminoglycoside antibiotics.
[37]	Campylobacter spp.	589	Retail poultry meat	The following AMR genes were identified: tetO, bla_OXA-61, aph(2″)-Ic, aph(2″)-If, aph(2″)-Ig, aph(3′)-III, ant(6)-1a, aadE, aph(3″)-VIIa, and Inu(C). Mutations in housekeeping genes (gyrA at position 86, 23S rRNA at position 2074 and 2075) associated with AMR phenotypes were also identified.
[38]	Campylobacter spp.	114	Humans, retail meats, and cecal samples from food production animals	Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2′)-If, aph(2″)-Ig, aph(2″)-Ih, aac(6′)-Ie-aph(2″)-Ia, aac(6′)-Ie-aph(2″)-If, aac(6′)-Im, aadE, sat4, ant(6′), aad9, aph(3′)-Ic, and aph(3′)-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA), were identified.
[26]	Campylobacter coli	2	Retail meats	A self-transmissible plasmid carrying multiple antibiotic resistance genes was identified, carrying genes encoding resistance to gentamicin, kanamycin, streptomycin, streptothricin, and tetracycline. Gentamicin resistance was due to a phosphotransferase gene, aph(2″)-Ig, not described previously.
[39]	Clostridium difficile	40	Human and porcine origin	AMR genotypes were characterized by resistance to tetracycline [tetM, tetA(P), tetB(P), and tetW], clindamycin/erythromycin (ermB), and aminoglycosides (aph3-III-Sat4A-ant6-Ia). Resistance was mediated by clinically important mobile genetic elements, most notably Tn6194 (harboring ermB) and a novel variant of Tn5397 (harboring tetM).
[40]	C. difficile	2	Ground pork	Identification of vancomycin (vanW, vanA, vanR, vanS, vex2, vex3, vncR, vncS); fluoroquinolones (gyrA and gyrB); tetracyclines (tetM, translation elongation factor G); beta-lactams (blaZ); and macrolides (macrolide efflux protein, macrolide glycosyltransferase) resistance genes, and multiple multidrug resistance efflux pump genes.
[31]	Enterococcus spp.	197	Various animal and food sources	Resistance genotypes correlated with resistance phenotypes in 96.5% of cases for the 11 drugs investigated.
[21]	Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Salmonella enterica serovar Typhimurium	200	Pigs	High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Correlation between MLST type and resistance profiles was only observed in S. enterica serovar Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates.
[41]	ESBL-producing Enterobacteriaceae	24	Fish and environmental samples	Nine of eleven sequenced fish isolates had the bla_CTX-M-15 gene, whereas 12/13 from environment carried bla_CTX-M-15. AMR genes encoding resistance to sulfonamides (sul1/sul2), tetracyclines [tet(A)/tet(B)], fluoroquinolones [e.g., aac(6′)-Ib-cr, qnrS1], aminoglycosides [e.g., aac(3)-lld, strB, strA], and trimethoprim (e.g., dfrA14) were detected.
[42]	E. coli	17	Retail chicken meat	All strains carried an IncK plasmid with a bla_CMY-2 gene.
[43]	E. coli	168	Broilers and free-range retail poultry (meat/ceca)	The prevalence rates of ESBL producing E. coli among broiler chicken were: meat 46%; ceca 40%. Whereas, those for free range chicken were: meat 15%; ceca 30%. E. coli from broiler and free-range chicken exhibited varied prevalence rates for multi-drug resistance (meat 68%; ceca 64% and meat 8%; ceca 26%, respectively).
[44]	E. coli	18	Dairy cow manure	All sequenced isolates carried at least one β-lactamase bla gene: TEM-1, TEM-81, CTX-M115, CTX-M15, OXA-1, or CMY-2. Several other AMR genes were detected in the sequenced isolates and all of them harbored AMR plasmids belonging to classic Inc groups.
[45]	E. coli	16	Swine farm	bla_NDM-5 and mcr-1 were located on two different plasmids, which showed 100% nucleotide identity in all 16 strains.
[46]	E. coli	26	Humans, cows, pigs, horse, rabbit, goat, environments and food	A total of 39 plasmids were identified. Eight plasmids carried resistance genes to aminoglycosides, carbapenems, penicillins, cephalosporins, chloramphenicol, dihydrofolate reductase inhibitors, sulfonamides, tetracyclines, and resistance to heavy metals. Two plasmids carried six of these resistance genes and two novel IncHI2 plasmids were also identified.
[47]	E. coli	42	Feedlot cattle	70% of the cattle strains carried at least one AMR gene
[48]	E. coli	3	Dairy cows	The mcr-1 gene (linked to colistin resistance) coexisted with multiple resistance genes in a plasmid (pXGE1mcr)
[49]	E. coli, Salmonella spp.	463	Retail meats and farm local samples	To improve the concordance between genotypic and phenotypic data, it was proposed to reduce the phenotypic cut-off values for streptomycin to ≥32 µg mL⁻¹ for both Salmonella and E. coli.
[50]	Helicobacter pullorum	4	Chicken meat	AMR-associated SNPs were detected (linked to resistance to fluoroquinolones, macrolides, and tetracyclines).
[51]	H. pullorum	11	Broiler and free-range chicken	WGS revealed the presence of five or six well characterized AMR genes, including those encoding a resistance-nodulation-division efflux pump
[30]	Klebsiella pneumoniae	7	Pig and human samples at abbatoirs	AMR genes associated with resistance to β-lactams, aminoglycosides, fluoroquinolones, macrolides, lincosamide, streptogramins, rifampicin, sulfonamides, trimethoprim, phenicols, and tetracycline were identified.
[29]	K. pneumoniae	44	Chicken, turkey and pork meat	Meat-source isolates were significantly more likely to be multidrug resistant and resistant to tetracycline and gentamicin than clinical isolates. Four sequence types occurred among both meat-source and clinical isolates.
[52]	Listeria monocytogenes	2	Ready-to-eat food	Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolones, tetracycline, penicillin, and macrolides were identified in the genomes of both strains.
[53]	L. monocytogenes	5	Environments from pork processing plants	Strains of a particular sequence type were shown to contain the BAC resistance transposon Tn6188, conveying resistance to quaternary ammonium compounds.
[54]	Proteus mirabilis	8	Food-producing animals	Seven integrative and conjugative elements were identical to ICEPmiJpn1, carrying the cephalosporinase gene bla_CMY-2.
[55]	Non-typhoidal Salmonella	536	Retail meat	A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. First finding of extended-spectrum β-lactamases (ESBLs) (bla_CTX-M1 and bla_SHV2a) in retail meat isolates of Salmonella in the United States.
[56]	Non-typhoidal Salmonella	1738	Animal, food and human sources	The Minimum Inhibitory Concentration (MIC) predictions were correlated with the ResFinder database. The genotypic cut-off values were established for 13 antimicrobials against Salmonella.
[20]	Non-typhoidal Salmonella	3491	Received by Public Health England’s Gastrointestinal Bacteria Reference Unit from different origins for surveillance purposes	Discrepancies between phenotypic and genotypic profiles for one or more antimicrobials were detected for 76 isolates (2.18%). Only 88/52,365 (0.17%) isolate/antimicrobial combinations were discordant. Pan-susceptibility to antimicrobials was observed in 2190 isolates (62.73%).
[33]	S. enterica	90	Dairy cattle and humans	Genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.2 and specificity of 85.2.
[57]	S. enterica serovar Typhimurium	984	Swine	Multiple genotypic resistance determinants were predominant, including resistance against ampicillin, streptomycin, sulfonamides, and tetracyclines. Phenotypic resistance to enrofloxacin and ceftiofur was found in conjunction with the presence of plasmid-mediated AMR genes.
[58]	S. enterica serovar Typhimurium	1	Swine carcass	The following AMR genes were identified: tetA, aac3IIa, aadA1, strA, strB, bla_TEM-1B, qnrE, sul1, drfA1, and floR.
[59]	S. enterica serovar Heidelberg	113	Humans, abbatoir poultry and retail poultry	CMY-2 plasmids, all belonging to incompatibility group I1, were identified in cefoxitin-resistant isolates. Analysis of IncI1 plasmid sequences revealed high identity (95% to 99%) to a previously described plasmid (pCVM29188_101) found in S. enterica serovar Kentucky.
[60]	S. enterica serovar Indiana	1	Poultry slaughterhouse	24 multi-drug resistance (MDR) genes, located on 4 plasmids, were identified, including the mcr-1 gene (linked to colistin resistance).
[61]	S. enterica serovar Infantis	12	Humans, food-producing animals and meat	Some isolates harbored a conjugative megaplasmid (~280–320 Kb) which carried the ESBL gene blaCTX-M-1, and additional genes [tet(A), sul1, dfrA1 and dfrA14] mediating cefotaxime, tetracycline, sulfonamide, and trimethoprim resistance.
[62]	S. enterica serovar Muenster	2	Dairy farm environments	The plasmid-mediated qnrB19 gene and IncR plasmid type were identified in both isolates.
[63]	S. enterica serovar Typhimurium	225	Humans, animals, feed, and food	The non-clinical use of narrow-spectrum penicillins (e.g., benzylpenicillin) might have favored the diffusion of plasmids carrying the bla_TEM-1 gene in S. enterica serotype Typhimurium in the late 1950s.
[64]	S. enterica serovar Typhimurium	4	Poultry and humans	The following AMR genes were identified: strA, strB, and aadA1 (aminoglycosides); bla_TEM-1B (β-lactams); catA1 (phenicols); sul1 and sul2 (sulphonamides); tet B (tetracyclines); and dfrA1 (trimethoprim).
[65]	S. enterica serovar Typhimurium and S. enterica serovar Kentucky	2	Chicken carcasses	A total of five plasmids conveying AMR genes were found.
[66]	S. enterica serovar Weltevreden	44	Human stool and contaminated food samples	AMR genes were only identified in eight isolates, linked to resistance to tetracycline, ciprofloxacin or ampicillin.
[67]	Staphylococcus aureus	66	Retail meats	Eleven spa types were represented. The majority of MRSA (84.8%) possessed SCCmec IV.
[68]	S. aureus	9	Pork, chicken and turkey meat	Multiple resistance genes/mutations were detected. All livestock-associated methicillin-resistant S. aureus (LA-MRSA) harbored tet(M) (±tet(K) and tet(L)), and only seven of these additionally harbored multi-drug resistance to beta-lactams, quinolones, and macrolides.
[69]	S. aureus	12	Livestock animals	Most isolates harbored resistance genes to ≥3 antimicrobial classes in addition to β-lactams. Heavy metal resistance genes were detected in most European ccrC positive isolates, with >80% harboring czrC, encoding zinc and cadmium resistance.
[70]	S. aureus	15	Bulk milk	A divergent mecA homologue (mecA_LGA251), later named as mecC, was identified.
[71]	Streptococcus thermophilus	5	Raw milk	tet(S) and ermB identified as determinants of AMR.
[72]	Carbapenem-resistant bacteria	28	Dairy cattle	Isolates included: 3 E. coli harboring bla_CMY-2 and truncated ompF genes; 8 Aeromonas harboring bla_cphA-like genes; 1 Acinetobacter baumannii harboring a novel bla_OXA gene (bla_OXA-497); and 6 Pseudomonas with conserved domains of various carbapenemase-producing genes.

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

Correction: Oniciuc, E. A.; et al. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes 2018, 9, 268.

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