Last data update: May 13, 2024. (Total: 46773 publications since 2009)
Records 1-18 (of 18 Records) |
Query Trace: McDermott PF[original query] |
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Genomic analysis of azithromycin-resistant Salmonella from food animals at slaughter and processing, and retail meats, 2011-2021, United States
Ge B , Mukherjee S , Li C , Harrison LB , Hsu CH , Tran TT , Whichard JM , Dessai U , Singh R , Gilbert JM , Strain EA , McDermott PF , Zhao S . Microbiol Spectr 2023 e0348523 Macrolides of different ring sizes are critically important antimicrobials for human medicine and veterinary medicine, though the widely used 15-membered ring azithromycin in humans is not approved for use in veterinary medicine. We document here the emergence of azithromycin-resistant Salmonella among the NARMS culture collections between 2011 and 2021 in food animals and retail meats, some with co-resistance to ceftriaxone or decreased susceptibility to ciprofloxacin. We also provide insights into the underlying genetic mechanisms and genomic contexts, including the first report of a novel combination of azithromycin resistance determinants and the characterization of multidrug-resistant plasmids. Further, we highlight the emergence of a multidrug-resistant Salmonella Newport clone in food animals (mainly cattle) with both azithromycin resistance and decreased susceptibility to ciprofloxacin. These findings contribute to a better understating of azithromycin resistance mechanisms in Salmonella and warrant further investigations on the drivers behind the emergence of resistant clones. |
Using the NCBI AMRFinder Tool to Determine Antimicrobial Resistance Genotype-Phenotype Correlations Within a Collection of NARMS Isolates (preprint)
Feldgarden M , Brover V , Haft DH , Prasad AB , Slotta DJ , Tolstoy I , Tyson GH , Zhao S , Hsu CH , McDermott PF , Tadesse DA , Morales C , Simmons M , Tillman G , Wasilenko J , Folster JP , Klimke W . bioRxiv 2019 550707 Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify acquired AMR genes in whole genome sequences, the National Center for Biotechnology Information (NCBI) has produced a high-quality, curated, AMR gene reference database consisting of up-to-date protein and gene nomenclature, a set of hidden Markov models (HMMs), and a curated protein family hierarchy. Currently, the Bacterial Antimicrobial Resistance Reference Gene Database contains 4,579 antimicrobial resistance gene proteins and more than 560 HMMs.Here, we describe AMRFinder, a tool that uses this reference dataset to identify AMR genes. To assess the predictive ability of AMRFinder, we measured the consistency between predicted AMR genotypes from AMRFinder against resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS). This included 5,425 Salmonella enterica, 770 Campylobacter spp., and 47 Escherichia coli phenotypically tested against various antimicrobial agents. Of 87,679 susceptibility tests performed, 98.4% were consistent with predictions.To assess the accuracy of AMRFinder, we compared its gene symbol output with that of a 2017 version of ResFinder, another publicly available resistance gene database. Most gene calls were identical, but there were 1,229 gene symbol differences between them, with differences due to both algorithmic differences and database composition. AMRFinder missed 16 loci that Resfinder found, while Resfinder missed 1,147 loci AMRFinder identified. Two missing drug classes from the 2017 version of ResFinder contributed 81% of missed loci. Based on these results, AMRFinder appears to be a highly accurate AMR gene detection system.Importance Antimicrobial resistance is a major public health problem. Traditionally, antimicrobial resistance has been identified using phenotypic assays. With the advent of genome sequencing, we now can identify resistance genes and deduce if an isolate could be resistant to antibiotics. We describe a database of 4,579 acquired antimicrobial resistance genes, the largest publicly available, and a software tool to identify genes in bacterial genomes, AMRFinder. Unlike other tools, AMRFinder uses a gene hierarchy to prevent overpredicting what the correct gene call should be, enabling more accurate assessment. To assess these resources, we determined the resistance gene content of over 6,200 bacterial isolates from the National Antimicrobial Resistance Monitoring System that have been assayed using traditional methods and that also have had their genomes sequenced. We also compared our gene assessments to those of a popularly used tool. We found that AMRFinder has a high overall consistency between genotypes and phenotypes. |
Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates.
Feldgarden M , Brover V , Haft DH , Prasad AB , Slotta DJ , Tolstoy I , Tyson GH , Zhao S , Hsu CH , McDermott PF , Tadesse DA , Morales C , Simmons M , Tillman G , Wasilenko J , Folster JP , Klimke W . Antimicrob Agents Chemother 2019 63 (11) Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify AMR genes in whole genome sequences, the National Center for Biotechnology Information (NCBI) has produced AMRFinder, a tool that identifies AMR genes using a high-quality curated AMR gene reference database. The Bacterial Antimicrobial Resistance Reference Gene Database consists of up-to-date gene nomenclature, a set of hidden Markov models (HMMs), and a curated protein family hierarchy. Currently, it contains 4,579 antimicrobial resistance proteins and more than 560 HMMs.Here, we describe AMRFinder and its associated database. To assess the predictive ability of AMRFinder, we measured the consistency between predicted AMR genotypes from AMRFinder and resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS). This included 5,425 Salmonella enterica, 770 Campylobacter spp., and 47 Escherichia coli phenotypically tested against various antimicrobial agents. Of 87,679 susceptibility tests performed, 98.4% were consistent with predictions.To assess the accuracy of AMRFinder, we compared its gene symbol output with that of a 2017 version of ResFinder, another publicly available resistance gene detection system. Most gene calls were identical, but there were 1,229 gene symbol differences (8.8%) between them, with differences due to both algorithmic differences and database composition. AMRFinder missed 16 loci that Resfinder found, while Resfinder missed 216 loci AMRFinder identified. Based on these results, AMRFinder appears to be a highly accurate AMR gene detection system. |
National Antimicrobial Resistance Monitoring System: Two Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance.
Karp BE , Tate H , Plumblee JR , Dessai U , Whichard JM , Thacker EL , Robertson Hale K , Wilson W , Friedman CR , Griffin PM , McDermott PF . Foodborne Pathog Dis 2017 14 (10) 545-557 Drug-resistant bacterial infections pose a serious and growing public health threat globally. In this review, we describe the role of the National Antimicrobial Resistance Monitoring System (NARMS) in providing data that help address the resistance problem and show how such a program can have broad positive impacts on public health. NARMS was formed two decades ago to help assess the consequences to human health arising from the use of antimicrobial drugs in food animal production in the United States. A collaboration among the Centers for Disease Control and Prevention, the U.S. Food and Drug Administration, the United States Department of Agriculture, and state and local health departments, NARMS uses an integrated "One Health" approach to monitor antimicrobial resistance in enteric bacteria from humans, retail meat, and food animals. NARMS has adapted to changing needs and threats by expanding surveillance catchment areas, examining new isolate sources, adding bacteria, adjusting sampling schemes, and modifying antimicrobial agents tested. NARMS data are not only essential for ensuring that antimicrobial drugs approved for food animals are used in ways that are safe for human health but they also help address broader food safety priorities. NARMS surveillance, applied research studies, and outbreak isolate testing provide data on the emergence of drug-resistant enteric bacteria; genetic mechanisms underlying resistance; movement of bacterial populations among humans, food, and food animals; and sources and outcomes of resistant and susceptible infections. These data can be used to guide and evaluate the impact of science-based policies, regulatory actions, antimicrobial stewardship initiatives, and other public health efforts aimed at preserving drug effectiveness, improving patient outcomes, and preventing infections. Many improvements have been made to NARMS over time and the program will continue to adapt to address emerging resistance threats, changes in clinical diagnostic practices, and new technologies, such as whole genome sequencing. |
Comparative Analysis of Extended Spectrum Beta- Lactamase CTX-M-65-Producing Salmonella Infantis Isolates from Humans, Food Animals, and Retail Chickens in the United States.
Tate H , Folster JP , Hsu CH , Chen J , Hoffmann M , Li C , Morales C , Tyson GH , Mukerjee S , Brown AC , Green A , Wilson W , Dessai U , Abbott J , Joseph L , Haro J , Ayers S , McDermott PF , Zhao S . Antimicrob Agents Chemother 2017 61 (7) We sequenced the genomes of ten Salmonella enterica serovar Infantis containing blaCTX-M-65 isolated from chicken, cattle, and human sources collected between 2012 and 2015 in the United States through routine NARMS surveillance and product sampling programs. We also completely assembled the plasmids from four of the isolates. All isolates had a D87Y mutation in the gyrA gene and harbored between 7 and 10 resistance genes (aph (4)-Ia, aac (3)-IVa, aph(3' )-Ic, blaCTX-M-65, fosA3, floR, dfrA14, sul1, tetA, aadA1) located in two distinct sites of a megaplasmid ( approximately 316-323kb) similar to that described in a blaCTX-M-65-positive S. Infantis isolated from a patient in Italy. High-quality single nucleotide polymorphism (hqSNP) analysis revealed that all U.S. isolates were closely related, separated by only 1 to 38 pairwise high quality SNPs, indicating a high likelihood that strains from humans, chicken, and cattle recently evolved from a common ancestor. The U.S. isolates were genetically similar to the blaCTX-M-65-positive S. Infantis isolate from Italy, with a separation of 34 to 47 SNPs. This is the first report of the blaCTX-M-65 gene and the pESI-like megaplasmid from S. Infantis in the United States, and illustrates the importance of applying a global One Health, human and animal perspective to combat antimicrobial resistance. |
MRSA and multidrug-resistant Staphylococcus aureus in U.S. retail meats, 2010–2011
Ge B , Mukherjee S , Hsu CH , Davis JA , Tran TTT , Yang Q , Abbott JW , Ayers SL , Young SR , Crarey ET , Womack NA , Zhao S , McDermott PF . Food Microbiol 2017 62 289-297 Methicillin-resistant Staphylococcus aureus (MRSA) has been detected in retail meats, although large-scale studies are scarce. We conducted a one-year survey in 2010–2011 within the framework of the National Antimicrobial Resistance Monitoring System. Among 3520 retail meats collected from eight U.S. states, 982 (27.9%) contained S. aureus and 66 (1.9%) were positive for MRSA. Approximately 10.4% (107/1032) of S. aureus isolates, including 37.2% (29/78) of MRSA, were multidrug-resistant (MDRSA). Turkey had the highest MRSA prevalence (3.5%), followed by pork (1.9%), beef (1.7%), and chicken (0.3%). Whole-genome sequencing was performed for all 66 non-redundant MRSA. Among five multilocus sequence types identified, ST8 (72.7%) and ST5 (22.7%) were most common and livestock-associated MRSA ST398 was assigned to one pork isolate. Eleven spa types were represented, predominately t008 (43.9%) and t2031 (22.7%). All four types of meats harbored t008, whereas t2031 was recovered from turkey only. The majority of MRSA (84.8%) possessed SCCmec IV and 62.1% harbored Panton-Valentine leukocidin. Pulsed-field gel electrophoresis showed that all ST8 MRSA belonged to the predominant human epidemic clone USA300, and others included USA100 and USA200. We conclude that a diverse MRSA population was present in U.S. retail meats, albeit at low prevalence. |
The use of whole genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella.
McDermott PF , Tyson GH , Kabera C , Chen Y , Li C , Folster JP , Ayers SL , Lam C , Tate HP , Zhao S . Antimicrob Agents Chemother 2016 60 (9) 5515-20 Laboratory-based in vitro antimicrobial susceptibility testing is the foundation for guiding anti-infective therapy and monitoring antimicrobial resistance trends. We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance determinants among strains of nontyphoidal Salmonella and correlated these with susceptibility phenotypes to evaluate the utility of WGS for antimicrobial resistance surveillance. Six hundred forty Salmonella of 43 different serotypes were selected from among retail meat and human clinical isolates that were tested for susceptibility to 14 antimicrobials using broth microdilution. The minimum inhibitory concentration (MIC) for each drug was used to categorize isolates as susceptible or resistant based on Clinical and Laboratory Standards Institute clinical breakpoints or NARMS consensus interpretive criteria. Each isolate was subjected to whole-genome shotgun sequencing, and resistance genes were identified from assembled sequences. A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. There were more unique resistance genes (n=59) in the 104 human isolates than in the 536 retail meat isolates (n=36). Overall, resistance genotypes and phenotypes correlated in 99.0% of cases. Correlations approached 100% for most classes of antibiotics, but were lower for aminoglycosides and beta-lactams. We report the first finding of ESBLs (blaCTX-M1 and blaSHV2a) in retail meat isolates of Salmonella in the U.S. Whole-genome sequencing is an effective tool for predicting antibiotic resistance in nontyphoidal Salmonella, although the use of more appropriate surveillance breakpoints and increased knowledge of new resistance alleles will further improve correlations. |
Antimicrobial resistance in Salmonella in the United States: 1948 - 1995
Tadesse DA , Singh A , Zhao S , Bartholomew M , Womack N , Ayers S , Fields PI , McDermott PF . Antimicrob Agents Chemother 2016 60 (4) 2567-71 We conducted a retrospective study of 2,149 clinical Salmonella strains to help document the historical emergence of antimicrobial resistance. There were significant increases in resistance to older drugs including ampicillin, chloramphenicol, streptomycin, sulfamethoxazole and tetracycline, which was most common in serotype Typhimurium. An increase in multidrug-resistance was observed for each decade since the 1950s. These data help show how Salmonella has evolved over the past six decades following the introduction of new antimicrobial agents. |
Whole Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter.
Zhao S , Tyson GH , Chen Y , Li C , Mukherjee S , Young S , Lam C , Folster JP , Whichard JM , McDermott PF . Appl Environ Microbiol 2015 82 (2) 459-66 OBJECTIVES: The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). METHODS: One hundred-fourteen Campylobacter sp. (82 C. coli and 32 C. jejuni) isolated from 2000-2013 from ill humans, retails meats and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth micro-dilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through BLASTx analysis. RESULTS: Eighteen resistance genes, including tetO, blaOXA-61, catA, lnuC, 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, aph(3')-IIIa, and mutations in two house-keeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin and ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. CONCLUSIONS: There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs. |
Novel gentamicin resistance genes in Campylobacter isolated from humans and retail meats in the USA.
Zhao S , Mukherjee S , Chen Y , Li C , Young S , Warren M , Abbott J , Friedman S , Kabera C , Karlsson M , McDermott PF . J Antimicrob Chemother 2015 70 (5) 1314-21 OBJECTIVES: To understand the molecular epidemiology of gentamicin-resistant Campylobacter and investigate aminoglycoside resistance mechanisms. METHODS: One-hundred-and-fifty-one gentamicin-resistant Campylobacter isolates from humans (n = 38 Campylobacter jejuni; n = 41, Campylobacter coli) and retail chickens (n = 72 C. coli), were screened for the presence of gentamicin resistance genes by PCR and subtyped using PFGE. A subset of the isolates (n = 41) was analysed using WGS. RESULTS: Nine variants of gentamicin resistance genes were identified: aph(2'')-Ib, Ic, Ig, If, If1, If3, Ih, aac(6')-Ie/aph(2'')-Ia and aac(6')-Ie/aph(2'')-If2. The aph(2'')-Ib, Ic, If1, If3, Ih and aac(6')-Ie/aph(2'')-If2 variants were identified for the first time in Campylobacter. Human isolates showed more diverse aminoglycoside resistance genes than did retail chicken isolates, in which only aph(2'')-Ic and -Ig were identified. The aph(2'')-Ig gene was only gene shared by C. coli isolates from human (n = 27) and retail chicken (n = 69). These isolates displayed the same resistance profile and similar PFGE patterns, suggesting that contaminated retail chicken was probably the source of human C. coli infections. Human isolates were genetically diverse and generally more resistant than the retail chicken isolates. The most frequent co-resistance was to tetracycline (78/79, 98.7%), followed by ciprofloxacin/nalidixic acid (46/79, 58.2%), erythromycin and azithromycin (36/79, 45.6%), telithromycin (32/79, 40.5%) and clindamycin (18/79, 22.8%). All human and retail meat isolates were susceptible to florfenicol. CONCLUSIONS: This study demonstrated that several new aminoglycoside resistance genes underlie the recent emergence of gentamicin-resistant Campylobacter, and that, in addition to contaminated retail chicken, other sources have also contributed to gentamicin-resistant Campylobacter infections in humans. |
Comparative genomic analysis and virulence differences in closely related salmonella enterica serotype heidelberg isolates from humans, retail meats, and animals.
Hoffmann M , Zhao S , Pettengill J , Luo Y , Monday SR , Abbott J , Ayers SL , Cinar HN , Muruvanda T , Li C , Allard MW , Whichard J , Meng J , Brown EW , McDermott PF . Genome Biol Evol 2014 6 (5) 1046-68 Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. Recently, an antibiotic-resistant strain of this serovar was implicated in a large 2011 multistate outbreak resulting from consumption of contaminated ground turkey that involved 136 confirmed cases, with one death. In this study, we assessed the evolutionary diversity of 44 S. Heidelberg isolates using whole-genome sequencing (WGS) generated by the 454 GS FLX (Roche) platform. The isolates, including 30 with nearly indistinguishable (one band difference) Xbal pulsed-field gel electrophoresis patterns (JF6X01.0032, JF6X01.0058), were collected from various sources between 1982 and 2011 and included nine isolates associated with the 2011 outbreak. Additionally, we determined the complete sequence for the chromosome and three plasmids from a clinical isolate associated with the 2011 outbreak using the Pacific Biosciences (PacBio) system. Using single-nucleotide polymorphism (SNP) analyses, we were able to distinguish highly clonal isolates, including strains isolated at different times in the same year. The isolates from the recent 2011 outbreak clustered together with a mean SNP variation of only 17 SNPs. The S. Heidelberg isolates carried a variety of phages, such as prophage P22, P4, lambda-like prophage Gifsy-2, and the P2-like phage which carries the sopE1 gene, virulence genes including 62 pathogenicity, and 13 fimbrial markers and resistance plasmids of the incompatibility (Inc)I1, IncA/C, and IncHI2 groups. Twenty-one strains contained an IncX plasmid carrying a type IV secretion system. On the basis of the recent and historical isolates used in this study, our results demonstrated that, in addition to providing detailed genetic information for the isolates, WGS can identify SNP targets that can be utilized for differentiating highly clonal S. Heidelberg isolates. |
Antimicrobial resistance genes in multidrug-resistant Salmonella enterica isolated from animals, retail meats, and humans in the United States and Canada.
Glenn LM , Lindsey RL , Folster JP , Pecic G , Boerlin P , Gilmour MW , Harbottle H , Zhao S , McDermott PF , Fedorka-Cray PJ , Frye JG . Microb Drug Resist 2013 19 (3) 175-84 Salmonella enterica is a prevalent foodborne pathogen that can carry multidrug resistance (MDR) and pose a threat to human health. Identifying the genetics associated with MDR in Salmonella isolated from animals, foods, and humans can help determine sources of MDR in food animals and their impact on humans. S. enterica serovars most frequently carrying MDR from healthy animals, retail meats, and human infections in the United States and Canada were identified and isolates resistant to the largest number of antimicrobials were chosen. Isolates were from U.S. slaughter (n=12), retail (9), and humans (9), and Canadian slaughter (9), retail (9), and humans (8; total n=56). These isolates were assayed by microarray for antimicrobial resistance and MDR plasmid genes. Genes detected encoded resistance to aminoglycosides (alleles of aac, aad, aph, strA/B); beta-lactams (blaTEM, blaCMY, blaPSE-1); chloramphenicol (cat, flo, cmlA); sulfamethoxazole (sulI); tetracycline (tet(A, B, C, D) and tetR); and trimethoprim (dfrA). Hybridization with IncA/C plasmid gene probes indicated that 27/56 isolates carried one of these plasmids; however, they differed in several variable regions. Cluster analysis based on genes detected separated most of the isolates into two groups, one with IncA/C plasmids and one without IncA/C plasmids. Other plasmid replicons were detected in all but one isolate, and included I1 (25/56), N (23/56), and FIB (10/56). The presence of different mobile elements along with similar resistance genes suggest that these genetic elements may acquire similar resistance cassettes, and serve as multiple sources for MDR in Salmonella from food animals, retail meats, and human infections. |
Characterization of extended-spectrum cephalosporin-resistant Salmonella enterica serovar Heidelberg isolated from food animals, retail meat, and humans in the United States 2009
Folster JP , Pecic G , Singh A , Duval B , Rickert R , Ayers S , Abbott J , McGlinchey B , Bauer-Turpin J , Haro J , Hise K , Zhao S , Fedorka-Cray PJ , Whichard J , McDermott PF . Foodborne Pathog Dis 2012 9 (7) 638-45 Salmonella enterica is one of the most common causes of foodborne illness in the United States. Although salmonellosis is usually self-limiting, severe infections typically require antimicrobial treatment, and ceftriaxone, an extended-spectrum cephalosporin (ESC), is commonly used in both adults and children. Surveillance conducted by the National Antimicrobial Resistance Monitoring System (NARMS) has shown a recent increase in ESC resistance among Salmonella Heidelberg isolated from food animals at slaughter, retail meat, and humans. ESC resistance among Salmonella in the United States is usually mediated by a plasmid-encoded bla(CMY) beta-lactamase. In 2009, we identified 47 ESC-resistant bla(CMY)-positive Heidelberg isolates from humans (n=18), food animals at slaughter (n=16), and retail meats (n=13) associated with a spike in the prevalence of this serovar. Almost 90% (26/29) of the animal and meat isolates were isolated from chicken carcasses or retail chicken meat. We screened NARMS isolates for the presence of bla(CMY), determined whether the gene was plasmid-encoded, examined pulsed-field gel electrophoresis patterns to assess the genetic diversities of the isolates, and categorized the bla(CMY) plasmids by plasmid incompatibility groups and plasmid multi-locus sequence typing (pMLST). All 47 bla(CMY) genes were found to be plasmid encoded. Incompatibility/replicon typing demonstrated that 41 were IncI1 plasmids, 40 of which only conferred bla(CMY)-associated resistance. Six were IncA/C plasmids that carried additional resistance genes. pMLST of the IncI1-bla(CMY) plasmids showed that 27 (65.8%) were sequence type (ST) 12, the most common ST among bla(CMY)-IncI1 plasmids from Heidelberg isolated from humans. Ten plasmids had a new ST profile, ST66, a type very similar to ST12. This work showed that the 2009 increase in ESC resistance among Salmonella Heidelberg was caused mainly by the dissemination of bla(CMY) on IncI1 and IncA/C plasmids in a variety of genetic backgrounds, and is likely not the result of clonal expansion. |
Plasmid-mediated quinolone resistance among non-Typhi Salmonella enterica isolates, USA
Sjolund-Karlsson M , Howie R , Rickert R , Krueger A , Tran TT , Zhao S , Ball T , Haro J , Pecic G , Joyce K , Fedorka-Cray PJ , Whichard JM , McDermott PF . Emerg Infect Dis 2010 16 (11) 1789-91 We determined the prevalence of plasmid-mediated quinolone resistance mechanisms among non-Typhi Salmonella spp. isolated from humans, food animals, and retail meat in the United States in 2007. Six isolates collected from humans harbored aac(6')Ib-cr or a qnr gene. Most prevalent was qnrS1. No animal or retail meat isolates harbored a plasmid-mediated mechanism. |
Multidrug-resistant Salmonella isolates from retail chicken meat compared with human clinical isolates
M'Ikanatha N M , Sandt CH , Localio AR , Tewari D , Rankin SC , Whichard JM , Altekruse SF , Lautenbach E , Folster JP , Russo A , Chiller TM , Reynolds SM , McDermott PF . Foodborne Pathog Dis 2010 7 (8) 929-34 AIM: To examine the prevalence of antimicrobial-resistant Salmonella in chicken meat and correlate with isolates from ill humans. METHODS: We isolated Salmonella from raw chicken purchased from a randomly selected sample of retail outlets in central Pennsylvania during 2006-2007. Salmonella isolates from meat were compared, using pulsed-field gel electrophoresis, to isolates in the PulseNet database of Salmonella recovered from humans. RESULTS: Of 378 chicken meat samples, 84 (22%) contained Salmonella. Twenty-six (31%) of the Salmonella isolates were resistant to > or = 3 antimicrobials and 18 (21%) were resistant to ceftiofur. All ceftiofur-resistant isolates exhibited reduced susceptibility (minimum inhibitory concentration >2 microg/mL) to ceftriaxone and carried a bla(CMY) gene, as detected by polymerase chain reaction. Among the 28 Salmonella serovar Typhimurium isolates, 20 (71.4%) were resistant to > or = 3 antimicrobials and 12 (42.9%) were resistant to ceftiofur. One ceftiofur-resistant Salmonella serovar Typhimurium poultry isolate exhibited a rare pulsed-field gel electrophoresis pattern indistinguishable from a human isolate in PulseNet; both isolates carried the bla(CMY-2) gene. CONCLUSIONS: These data demonstrate the presence of multidrug-resistant Salmonella in poultry meat, including bla(CMY) plasmid-mediated genes that confer resistance to both ceftiofur, used in poultry, and ceftriaxone, used for treating salmonellosis in humans. This study illustrates the potential for molecular subtyping databases to identify related Salmonella isolates from meat and ill humans, and suggests that chicken could be a source for multidrug-resistant salmonellosis in humans. |
Evaluation of antimicrobial resistance phenotypes for predicting multidrug-resistant salmonella recovered from retail meats and humans in the United States
Whichard JM , Medalla F , Hoekstra RM , McDermott PF , Joyce K , Chiller T , Barrett TJ , White DG . J Food Prot 2010 73 (3) 445-51 Although multidrug-resistant (MDR) non-Typhi Salmonella (NTS) strains are a concern in food production, determining resistance to multiple antimicrobial agents at slaughter or processing may be impractical. Single antimicrobial resistance results for predicting multidrug resistance are desirable. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value were used to determine each antimicrobial agent's ability to predict MDR phenotypes of human health significance: ACSSuT (resistance to at least ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, tetracycline) in NTS isolates, and MDR-AmpC-SN (resistance to ACSSuT, additional resistance to amoxicillin-clavulanate and to ceftiofur, and decreased susceptibility [MIC ≥ 2 mug/ml] to ceftriaxone) in NTS serotype Newport. The U.S. National Antimicrobial Resistance Monitoring System determined MICs to 15 or more antimicrobial agents for 9,955 NTS isolates from humans from 1999 to 2004 and 689 NTS isolates from retail meat from 2002 to 2004. A total of 847 (8.5%) human and 26 (3.8%) retail NTS isolates were ACSSuT; 995 (10.0%) human and 16 (2.3%) retail isolates were serotype Newport. Among Salmonella Newport, 204 (20.5%) human and 9 (56.3%) retail isolates were MDR-AmpC-SN. Chloramphenicol resistance provided the highest PPVs for ACSSuT among human (90.5%; 95% confidence interval, 88.4 to 92.3) and retail NTS isolates (96.3%; 95% confidence interval, 81.0 to 99.9). Resistance to ceftiofur and to amoxicillin-clavulanate and decreased susceptibility to ceftriaxone provided the highest PPVs (97.1, 98.1, and 98.6%, respectively) for MDR-AmpC-SN from humans. High PPVs for these agents applied to retail meat MDR-AmpC-SN, but isolate numbers were lower. Variations in MIC results may complicate ceftriaxone's predictive utility. Selecting specific antimicrobial resistance offers practical alternatives for predicting MDR phenotypes. Chloramphenicol resistance works best for ACSSuT-NTS, and resistance to ceftiofur, amoxicillin-clavulanate, or chloramphenicol works best for MDR-AmpC-SN. |
Characterization of extended-spectrum cephalosporin-resistant salmonella enterica serovar heidelberg isolated from humans in the United States
Folster JP , Pecic G , Bolcen S , Theobald L , Hise K , Carattoli A , Zhao S , McDermott PF , Whichard JM . Foodborne Pathog Dis 2009 7 (2) 181-7 During the past decade, extended-spectrum cephalosporin resistance has increased among human isolates of Salmonella enterica serovar Heidelberg, the fourth most common serotype in the United States. We therefore characterized 54 Heidelberg isolates with decreased susceptibility (minimum inhibitory concentrations ≥2 mg/L) to ceftriaxone or ceftiofur; 49 (90.7%) contained the CMY-type beta-lactamase (bla(CMY)) gene. The 49 bla(CMY)-positive human Heidelberg isolates demonstrated a high degree of relatedness; 4 clusters (25 isolates total) had indistinguishable XbaI and BlnI patterns by pulsed-field gel electrophoresis and were indistinguishable from 42 retail meat Heidelberg isolates. Further characterization of 15 of these isolates demonstrated that all of the bla genes were bla(CMY-2) and plasmid-encoded, and most (11/15) of the plasmids were approximately 100 kb in size and belong to the incompatibility group I1 (IncI1). All five IncI1 plasmids tested by plasmid multilocus sequence typing analysis were ST12. This report suggests that extended-spectrum cephalosporin resistance among human Heidelberg isolates is mediated by the spread of a common IncI1 bla(CMY-2) plasmid, which may have a preference for a particular genetic background. |
Antimicrobial Resistance-Conferring Plasmids with Similarity to Virulence Plasmids from Avian Pathogenic Escherichia coli Strains in Salmonella enterica Serovar Kentucky Isolates from Poultry
Fricke WF , McDermott PF , Mammel MK , Zhao S , Johnson TJ , Rasko DA , Fedorka-Cray PJ , Pedroso A , Whichard JM , Leclerc JE , White DG , Cebula TA , Ravel J . Appl Environ Microbiol 2009 75 (18) 5963-71 Salmonella enterica, a leading cause of foodborne gastroenteritis worldwide, may be found in any raw food of animal, vegetable or fruit origin. Different Salmonella serovars vary in their distribution, virulence and host specificity. S. enterica serovar Kentucky (S. Kentucky), though often found in the food supply, is less commonly isolated from ill humans. The multidrug-resistant (MDR) isolate Salmonella Kentucky CVM29188, isolated from a chicken breast sample in 2003, contains three plasmids (146,811 bp; 101,461 bp; 46,121 bp), two of which carry resistance determinants (pCVM29188_146: strAB, tetRA and pCVM29188_101: blaCMY-2, sugE). Both resistance plasmids were transferable by conjugation, alone or in combination, to S. Kentucky, S. Newport and E. coli recipients. pCVM29188_146 shares a highly conserved plasmid backbone of 106 kb (>90% nucleotide identity) with two virulence plasmids from Avian Pathogenic Escherichia coli strains (pAPEC-O1-ColBM and pAPEC-O2-ColV). Shared APEC virulence factors include iutA/iucABCD, sitABCD, etsABC, iss, and iroBCDEN. PCR analyses of recent (1997-2005) S. Kentucky isolates from food animal, retail meat and human sources revealed that 172 (60%) contained a similar APEC-like plasmid backbone. Notably, though rare in human- and cattle-derived isolates, this plasmid backbone was found at high frequency (50-100%) among S. Kentucky isolates from chickens within the same time span. 94% of the APEC-positive isolates showed resistance to tetracycline and streptomycin. Together, our findings of a resistance-encoding APEC virulence plasmid in a poultry-derived S. Kentucky isolate and of similar resistance/virulence plasmids in most recent S. Kentucky isolates from chickens and, to lesser degree, from humans and cattle highlight the need for additional research in order to examine the prevalence and spread of combined virulence and resistance plasmids in bacteria in agricultural, environmental and clinical settings. |
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