High Prevalence of ESBL and Plasmid-Mediated Quinolone Resistance Genes in Salmonella enterica Isolated from Retail Meats and Slaughterhouses in Egypt.
ABSTRACT: The emergence and spread of multidrug-resistant Salmonella enterica (S. enterica) to humans through food of animal origin are considered a major global public health concern. Currently, little is known about the prevalence of important antimicrobial resistance genes in S. enterica from retail food in Africa. Therefore, the screening and characterization of the extended-spectrum β-lactamase (ESBL) and plasmid-mediated quinolone resistance (PMQR) genes in S. enterica isolated from retail meats and slaughterhouses in Egypt were done by using PCR and DNA sequencing techniques. Twenty-eight out of thirty-four (82.4%) non-duplicate S. enterica isolates showed multidrug-resistance phenotypes to at least three classes of antimicrobials, and fourteen (41.2%) exhibited an ESBL-resistance phenotype and harbored at least one ESBL-encoding gene. The identified β-lactamase-encoding genes included blaCTX-M-1, blaCTX-M-3, blaCTX-M-13, blaCTX-M-14, blaCTX-M-15, and blaSHV-12 (ESBL types); blaCMY-2 (AmpC type); and blaTEM-1 and blaOXA-1 (narrow-spectrum types). PMQR genes (included qnrA, qnrB, qnrS, and aac(6')-Ib-cr) were identified in 23 (67.6%) isolates. The presence of ESBL- and PMQR-producing S. enterica with a high prevalence rate in retail meats and slaughterhouses is considered a major threat to public health as these strains with resistance genes could be transmitted to humans through the food chain.
Project description:A total of 2,283 <i>Salmonella</i> isolates were recovered from 18,334 samples, including samples from patients with diarrhea, food of animal origin, and pets, across 5 provinces of China. The highest prevalence of <i>Salmonella</i> spp. was detected in chicken meats (39.3%, 486/1,237). Fifteen serogroups and 66 serovars were identified, with <i>Salmonella enterica</i> serovars Typhimurium and Enteritidis being the most dominant. Most (85.5%, 1,952/2,283) isolates exhibited resistance to??1 antimicrobial, and 56.4% were multidrug resistant (MDR). A total of 222 isolates harbored extended-spectrum ?-lactamases (ESBLs), and 200 of these were of the CTX-M type and were mostly detected in isolates from chicken meat and turtle fecal samples. Overall, eight <i>bla</i> <sub>CTX-M</sub> genes were identified, with <i>bla</i> <sub>CTX-M-65</sub>, <i>bla</i> <sub>CTX-M-123</sub>, <i>bla</i> <sub>CTX-M-14</sub>, <i>bla</i> <sub>CTX-M-79</sub>, and <i>bla</i> <sub>CTX-M-130</sub> being the most prevalent. In total, 166 of the 222 ESBL-producing isolates had amino acid substitutions in GyrA (S83Y, S83F, D87G, D87N, and D87Y) and ParC (S80I), while the plasmid-mediated quinolone resistance (PMQR)-encoding genes <i>oqxA</i>, <i>oqxB</i>, <i>qepA</i>, <i>qnrB</i>, and <i>qnrS</i> were detected in almost all isolates. Of the 15 sequence types (STs) identified in the 222 ESBLs, ST17, ST11, ST34, and ST26 ranked among the top 5 in number of isolates. Our study revealed considerable serovar diversity and a high prevalence of the co-occurrence of MDR determinants, including CTX-M-type ESBLs, quinolone resistance-determining region (QRDR) mutations, and PMQR genes. This is the first report of CTX-M-130 <i>Salmonella</i> spp. from patients with diarrhea and QRDR mutations from turtle fecal samples. Our study emphasizes the importance of actions, both in health care settings and in the veterinary medicine sector, to control the dissemination of MDR, especially the CTX-M-type ESBL-harboring <i>Salmonella</i> isolates.
Project description:The present study aimed to characterize the extended-spectrum β-lactamases and plasmid-mediated AmpC β-lactamases (ESBL/PMAβ) among <i>Escherichia coli</i> producers isolated from beef, pork, and poultry meat collected at retail, in Portugal. A total of 638 meat samples were collected and inoculated on selective medium for the search of <i>E. coli</i> resistant to 3rd generation cephalosporins. Isolates were characterized by antimicrobial susceptibility testing, molecular assays targeting ESBL/AmpC, plasmid-mediated quinolone resistance (PMQR), and plasmid-mediated colistin resistance (PMCR) encoding genes. The highest frequency of <i>E. coli</i> non-wild type to 3rd generation cephalosporins and fluoroquinolones was observed in broiler meat (30.3% and 93.3%, respectively). Overall, a diversity of acquired resistance mechanisms, were detected: <i>bla</i><sub>ESBL</sub> [<i>bla</i><sub>CTX-M-1</sub> (<i>n</i> = 19), <i>bla</i><sub>CTX-M-15</sub> (<i>n</i> = 4), <i>bla</i><sub>CTX-M-32</sub> (<i>n</i> = 12), <i>bla</i><sub>CTX-M-55</sub> (<i>n</i> = 8), <i>bla</i><sub>CTX-M-65</sub> (<i>n</i> = 4), <i>bla</i><sub>CTX-M-27</sub> (<i>n</i> = 2), <i>bla</i><sub>CTX-M-9</sub> (<i>n</i> = 1), <i>bla</i><sub>CTX-M-14</sub> (<i>n</i> = 11), <i>bla</i><sub>SHV-12</sub> (<i>n</i> = 27), <i>bla</i><sub>TEM-52</sub> (<i>n</i> = 1)], <i>bla</i><sub>PMAβ</sub> [<i>bla</i><sub>CMY-2</sub> (<i>n</i> = 8)], PMQR [<i>qnrB</i> (<i>n</i> = 27), <i>qnrS</i> (<i>n</i> = 21) and <i>aac(6')-Ib-type</i> (<i>n</i> = 4)] and PMCR [<i>mcr-1</i> (<i>n</i> = 8)]. Our study highlights that consumers may be exposed through the food chain to multidrug-resistant <i>E. coli</i> carrying diverse plasmid-mediated antimicrobial resistance genes, posing a great hazard to food safety and a public health risk.
Project description:<i>Salmonella enterica</i> remains one of the leading causes of foodborne bacterial disease. Retail meat is a major source of human salmonellosis. However, comparative genomic analyses of <i>S. enterica</i> isolates from retail meat from different sources in China are lacking. A total of 341 <i>S. enterica</i> strains were isolated from retail meat in sixteen districts of Beijing, China, at three different time points (January 1st, May 1st, and October 1st) in 2017. Comparative genomics was performed to investigate the genetic diversity, virulence and antimicrobial resistance gene (ARG) profiles of these isolates. The most common serotype was <i>S.</i> Enteritidis (203/341, 59.5%), which dominated among isolates from three different time points during the year. Laboratory retesting confirmed the accuracy of the serotyping results predicted by the <i>Salmonella In Silico</i> Typing Resource (SISTR) (96.5%). The pangenome of the 341 <i>S. enterica</i> isolates contained 13,931 genes, and the core genome contained 3,635 genes. Higher <i>Salmonella phage 118970 sal3</i> (219/341, 64.2%) and <i>Gifsy-2</i> (206/341, 60.4%) prevalence contributed to the diversity of the accessory genes, especially those with unknown functions. IncFII(S), IncX1, and IncFIB(S) plasmid replicons were more common in these isolates and were major sources of horizontally acquired foreign genes. The virulence gene profile showed fewer virulence genes associated with type III secretion systems in certain isolates from chicken. A total of 88 different ARGs were found in the 341 isolates. Three beta-lactamases, namely, <i>bla</i> <sub><i>CTX</i></sub> <sub>-</sub> <sub><i>M</i></sub> <sub>-</sub> <sub>55</sub> (<i>n</i> = 15), <i>bla</i> <sub><i>CTX</i></sub> <sub>-</sub> <sub><i>M</i></sub> <sub>-</sub> <sub>14</sub> (<i>n</i> = 11), <i>and bla</i> <sub><i>CTX</i></sub> <sub>-</sub> <sub><i>M</i></sub> <sub>-</sub> <sub>65</sub> (<i>n</i> = 11), were more prevalent in retail meats. The emergence of <i>qnrE1</i> and <i>bla</i> <sub><i>CTX</i></sub> <sub>-</sub> <sub><i>M</i></sub> <sub>-</sub> <sub>123</sub> indicated a potential increase in the prevalence of retail meats. After the prohibition of colistin in China, three and four isolates were positive for the colistin resistance genes <i>mcr-1.1</i> and <i>mcr-9</i>, respectively. Thus, we explored the evolution and genomic features of <i>S. enterica</i> isolates from retail meats in Beijing, China. The diverse ARGs of these isolates compromise food security and are a clinical threat.
Project description:Extended-spectrum β-lactamases (ESBLs) confer resistance to extended-spectrum cephalosporins, a major class of clinical antimicrobial drugs. We used genomic analysis to investigate whether domestic food animals, retail meat, and pets were reservoirs of ESBL-producing Salmonella for human infection in Canada. Of 30,303 Salmonella isolates tested during 2012-2016, we detected 95 ESBL producers. ESBL serotypes and alleles were mostly different between humans (n = 54) and animals/meat (n = 41). Two exceptions were bla<sub>SHV-2</sub> and bla<sub>CTX-M-1</sub> IncI1 plasmids<sub>,</sub> which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-bla<sub>SHV-2</sub> plasmid differed by only 1-7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying bla<sub>CTX-M-65</sub>, which has since emerged in poultry in other countries. There were few instances of similar isolates and plasmids, suggesting that domestic animals and retail meat might have been minor reservoirs of ESBL-producing Salmonella for human infection.
Project description:Widespread dissemination of extended-spectrum beta-lactamase (ESBL) <i>Escherichia coli</i> (<i>E. coli</i>) in animals, retail meats, and patients has been reported worldwide except for limited information on small ruminants. Our study focused on the genotypic characterization of ESBL <i>E. coli</i> from healthy sheep and their abattoir environment in North Carolina, USA. A total of 113 ESBL <i>E. coli</i> isolates from sheep (n = 65) and their abattoir environment (n = 48) were subjected to whole-genome sequencing (WGS). Bioinformatics tools were used to analyze the WGS data. Multiple CTX-M-type beta-lactamase genes were detected, namely <i>bla</i><sub>CTX-M-1</sub>, <i>bla</i><sub>CTX-M-14</sub>, <i>bla</i><sub>CTX-M-15</sub>, <i>bla</i><sub>CTX-M-27</sub>, <i>bla</i><sub>CTX-M-32</sub>, <i>bla</i><sub>CTX-M-55</sub>, and <i>bla</i><sub>CTX-M-65</sub>. Other beta-lactamase genes detected included <i>bla</i><sub>CMY-2</sub>, <i>bla</i><sub>TEM-1A/B/C</sub>, and <i>bla</i><sub>CARB-2</sub>. In addition, antimicrobial resistance (AMR) genes and/or point mutations that confer resistance to quinolones, aminoglycosides, phenicols, tetracyclines, macrolides, lincosamides, and folate-pathway antagonists were identified. The majority of the detected plasmids were shared between isolates from sheep and the abattoir environment. Sequence types were more clustered around seasonal sampling but dispersed across sample types. In conclusion, our study reported wide dissemination of ESBL <i>E. coli</i> in sheep and the abattoir environment and associated AMR genes, point mutations, and plasmids. This is the first comprehensive AMR and WGS report on ESBL <i>E. coli</i> from sheep and abattoir environments in the United States.
Project description:Salmonella enterica serovars have been isolated from Colombian broilers and broiler meat. The aim of this study was to investigate the diversity of ESBL/pAmpC genes in extended-spectrum cephalosporin resistant Salmonella enterica and the phylogeny of ESBL/pAmpC-carrying Salmonella using Whole Genome Sequencing (WGS). A total of 260 cefotaxime resistant Salmonella isolates, obtained between 2008 and 2013 from broiler farms, slaughterhouses and retail, were included. Isolates were screened by PCR for ESBL/pAmpC genes. Gene and plasmid subtyping and strain Multi Locus Sequence Typing was performed in silico for a selection of fully sequenced isolates. Core-genome-based analyses were performed per ST encountered. bla CMY-2-like was carried in 168 isolates, 52 carried bla CTX-M-2 group, 7 bla SHV, 5 a combination of bla CMY-2-like-bla SHV and 3 a combination of bla CMY-2-like-bla CTX-M-2 group. In 25 isolates no ESBL/pAmpC genes that were screened for were found. WGS characterization of 36 selected strains showed plasmid-encoded bla CMY-2 in 21, bla CTX-M-165 in 11 and bla SHV-12 in 7 strains. These genes were mostly carried on IncI1/ST12, IncQ1, and IncI1/ST231 plasmids, respectively. Finally, 17 strains belonged to S. Heidelberg ST15, 16 to S. Paratyphi B variant Java ST28, 1 to S. Enteritidis ST11, 1 to S. Kentucky ST152 and 1 to S. Albany ST292. Phylogenetic comparisons with publicly available genomes showed separate clustering of Colombian S. Heidelberg and S. Paratyphi B var. Java. In conclusion, resistance to extended-spectrum cephalosporins in Salmonella from Colombian poultry is mainly encoded by bla CMY-2 and bla CTX-M-165 genes. These genes are mostly associated with IncI1/ST12 and IncQ1 plasmids, respectively. Evolutionary divergence is observed between Colombian S. Heidelberg and S. Paratyphi B var. Java and those from other countries.
Project description:Genetic context of extended spectrum ?-Lactamase (ESBL) producing <i>Enterobacterales</i> and its association with plasmid mediated quinolone resistance (PMQR), aminoglycoside modifying enzymes (AME) and Trimethoprim/Sulfamethoxazole (TMP-SMX) resistance is little known from North India. Therefore, the current study was aimed to investigate the frequency of Non-?-Lactam antibiotic resistance associated genes in extended spectrum ?-Lactamase producing <i>Enterobacterales</i>. For this study, Non-Duplicate phenotypically confirmed ESBL producing <i>Enterobacterales</i> isolates (N = 186) were analyzed for ESBLs, PMQRs, AMEs and TMP-SMX resistance genes using polymerase chain reaction (PCR). PCR detected presence of PMQR genes in 81.29% (N = 139) of ESBL isolates (N = 171), AME genes in 60.82% and TMP-SMX resistance genes in 63.74% of the isolates. Molecular characterization of ESBL producing <i>Enterobacterales</i> showed 84.79% <i>bla<sub>TEM</sub></i> followed by 73.68% <i>bla<sub>CTX-M</sub></i>, 43.86% <i>bla<sub>SHV</sub></i>, 19.88% <i>bla<sub>PER</sub> and</i> 9.94% <i>bla<sub>VEB</sub></i>, respectively. Analysis of PMQR genes revealed 77.7% <i>aac(6')-lb-cr</i> the most commonly detected gene followed by 67.63% <i>oqxB</i>, 62.59% <i>oqxA,</i> 43.17% <i>qnrB</i>, 19.42% <i>qnrD,</i> 18.7% <i>qnrS</i>, 9.35% <i>qnrA</i>, 3.6% <i>qepA</i> and 2.88% <i>qnrC</i>, respectively. Analysis of AMEs gene profile demonstrated 81.73% <i>aac(6')-Ib</i>, the most frequently encountered gene followed by 46.15% <i>aph(3')-Ia,</i> 44.23% <i>ant(3")-Ia,</i> respectively. A 100% prevalence of <i>sul1,</i> followed by <i>dfrA</i> (54.63%) and <i>sul2</i> (15.74%) was observed. In summary, prevalence of ESBL-Producing genes (particularly <i>bla<sub>TEM</sub></i> and <i>bla<sub>CTX-M</sub></i>) along with PMQR, AMEs, and TMP-SMX resistant genes may potentially aid in the transfer of antimicrobial resistance among these strains.
Project description:Extended-spectrum β-lactamases (ESBLs) confer resistance to clinically important third-generation cephalosporins, which are often used to treat invasive salmonellosis. In the United States, ESBLs are rarely found in Salmonella. However, in 2014, the US Food and Drug Administration found bla<sub>CTX-M-65</sub> ESBL-producing Salmonella enterica serotype Infantis in retail chicken meat. The isolate had a rare pulsed-field gel electrophoresis pattern. To clarify the sources and potential effects on human health, we examined isolates with this pattern obtained from human surveillance and associated metadata. Using broth microdilution for antimicrobial susceptibility testing and whole-genome sequencing, we characterized the isolates. Of 34 isolates, 29 carried the bla<sub>CTX-M-65</sub> gene with <9 additional resistance genes on 1 plasmid. Of 19 patients with travel information available, 12 (63%) reported recent travel to South America. Genetically, isolates from travelers, nontravelers, and retail chicken meat were similar. Expanded surveillance is needed to determine domestic sources and potentially prevent spread of this ESBL-containing plasmid.
Project description:Non-typhoidal <i>Salmonella enterica</i> is an important gastrointestinal pathogen causing a considerable burden of disease. Resistance to third generation cephalosporins poses a serious threat for treatment of severe infections. In this study occurrence, phylogenetic relationship, and mechanisms of third generation cephalosporin resistance were investigated for clinical non-typhoidal <i>S. enterica</i> isolates in Germany. From 2017 to 2019, we detected 168 unique clinical <i>S. enterica</i> isolates with phenotypic resistance to third generation cephalosporins in a nation-wide surveillance. Compared to previous years, we observed a significant (<i>P</i>=0.0002) and consistent increase in resistant isolates from 0.41 % in 2005 to 1.71 % in 2019. In total, 34 different serovars were identified, most often <i>S</i>. Infantis (<i>n</i>=41; 24.4 %), <i>S</i>. Typhimurium (<i>n</i>=27; 16.1 %), <i>S</i>. Kentucky (<i>n</i>=21; 12.5 %), and <i>S</i>. Derby (<i>n</i>=17; 10.1 %). Whole genome analyses revealed extended-spectrum β-lactamase (ESBL) genes as main cause for third generation cephalosporin resistance, and most prevalent were <i>bla</i> <sub>CTX-M-1</sub> (<i>n</i>=55), <i>bla</i> <sub>CTX-M-14</sub> (<i>n</i>=25), and <i>bla</i> <sub>CTX-M-65</sub> (<i>n</i>=23). There was no strict correlation between serovar, phylogenetic lineage, and ESBL type but some serovar/ESBL gene combinations were detected frequently, such as <i>bla</i> <sub>CTX-M-1</sub> and <i>bla</i> <sub>CTX-M-65</sub> in <i>S</i>. Infantis or <i>bla</i> <sub>CTX-M-14b</sub> in <i>S</i>. Kentucky. The ESBL genes were mainly located on plasmids, including IncI, IncA/C variants, emerging pESI variants, and a novel <i>bla</i> <sub>CTX-M-1</sub>harbouring plasmid. We conclude that third generation cephalosporin resistance is on the rise among clinical <i>S. enterica</i> isolates in Germany, and occurrence in various <i>S. enterica</i> serovars is most probably due to multiple acquisition events of plasmids.
Project description:The purpose of this study was to determine the prevalence and molecular characterization of plasmid-mediated quinolone resistance (PMQR) genes (qnrA, qnrB, qnrS, aac(6')-Ib-cr, and qepA) among ESBL-producing Klebsiella pneumoniae isolates in Kashan, Iran. A total of 185 K. pneumoniae isolates were tested for quinolone resistance and ESBL-producing using the disk diffusion method and double disk synergy (DDST) confirmatory test. ESBL-producing strains were further evaluated for the bla CTX-M genes. The PCR method was used to show presence of plasmid-mediated quinolone resistance genes and the purified PCR products were sequenced. Eighty-seven ESBL-producing strains were identified by DDST confirmatory test and majority (70, 80.5%) of which carried bla CTX-M genes including CTX-M-1 (60%), CTX-M-2 (42.9%), and CTX-M-9 (34.3%). Seventy-seven ESBL-producing K. pneumoniae isolates harbored PMQR genes, which mostly consisted of aac(6')-Ib-cr (70.1%) and qnrB (46.0%), followed by qnrS (5.7%). Among the 77 PMQR-positive isolates, 27 (35.1%) and 1 (1.3%) carried 2 and 3 different PMQR genes, respectively. However, qnrA and qepA were not found in any isolate. Our results highlight high ESBL occurrence with CTX-M type and high frequency of plasmid-mediated quinolone resistance genes among ESBL-producing K. pneumoniae isolates in Kashan.