One Health Genomic Analysis of Extended-Spectrum β-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016.
ABSTRACT: 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 blaSHV-2 and blaCTX-M-1 IncI1 plasmids, which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-blaSHV-2 plasmid differed by only 1-7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying blaCTX-M-65, 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: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:The emergence and spread of multidrug-resistant <i>Salmonella enterica</i> (<i>S. enterica</i>) 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 <i>S. enterica</i> 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 <i>S. enterica</i> 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 <i>S. enterica</i> 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 <i>bla</i><sub>CTX-M-1</sub>, <i>bla</i><sub>CTX-M-3</sub>, <i>bla</i><sub>CTX-M-13</sub>, <i>bla</i><sub>CTX-M-14</sub>, <i>bla</i><sub>CTX-M-15</sub>, and <i>bla</i><sub>SHV-12</sub> (ESBL types); <i>bla</i><sub>CMY-2</sub> (AmpC type); and <i>bla</i><sub>TEM-1</sub> and <i>bla</i><sub>OXA-1</sub> (narrow-spectrum types). PMQR genes (included <i>qnrA</i>, <i>qnrB</i>, <i>qnrS</i>, and <i>aac(6')-Ib-cr</i>) were identified in 23 (67.6%) isolates. The presence of ESBL- and PMQR-producing <i>S. enterica</i> 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: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: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:Resistance of bacteria to 3<sup>rd</sup> generation cephalosporins mediated by beta-lactamases (ESBL, pAmpC) is a public health concern. In this study, 1517 phenotypically cephalosporin-resistant <i>E. coli</i> were screened for the presence of <i>bla</i><sub>SHV</sub> genes. Respective genes were detected in 161 isolates. Majority (91%) were obtained from poultry production and meat. The SHV-12 beta-lactamase was the predominant variant (<i>n</i> = 155), while the remaining isolates exhibited SHV-2 (<i>n</i> = 4) or SHV-2a (<i>n</i> = 2). A subset of the isolates (<i>n</i> = 51) was further characterized by PCR, PFGE, or whole-genome sequencing and bioinformatics analysis. The SHV-12-producing isolates showed low phylogenetic relationships, and dissemination of the <i>bla</i><sub>SHV-12</sub> genes seemed to be mainly driven by horizontal gene transfer. In most of the isolates, <i>bla</i><sub>SHV-12</sub> was located on transferable IncX3 (~43 kb) or IncI1 (~100 kb) plasmids. On IncX3, <i>bla</i><sub>SHV-12</sub> was part of a Tn6 composite transposon located next to a Tn3 transposon, which harbored the fluoroquinolone resistance gene <i>qnrS1</i>. On IncI1 plasmids, <i>bla</i><sub>SHV-12</sub> was located on an incomplete class 1 integron as part of a Tn21 transposon. In conclusion, SHV-12 is widely distributed in German poultry production and spreads via horizontal gene transfer. Consumers are at risk by handling raw poultry meat and should take care in appropriate kitchen hygiene.
Project description:Extended-spectrum ?-lactamase (ESBL)-producing Salmonella are one of the most important public health problems in developed countries. ESBL-producing Salmonella strains have been isolated from humans in Asian countries neighboring Japan, along with strains harboring the plasmid-mediated extended-spectrum cephalosporin (ESC)-resistance gene, ampC (pAmpC). However, only a few studies have investigated the prevalence of ESC-resistant Salmonella in chicken products in Japan, which are the main vehicle of Salmonella transmission. The aim of this study was to investigate the prevalence of ESBL-producing, pAmpC-harboring, or carbapenem-resistant Salmonella in chicken products in Japan. In total, 355 out of 779 (45.6%) chicken product samples collected from 1996-2010 contained Salmonella, resulting in 378 distinct isolates. Of these isolates, 373 were tested for resistance to ESCs, cephamycins, or carbapenems. Isolates that showed resistance to one or more of these antimicrobials were then examined by PCR and DNA sequence analysis for the presence of the bla(CMY), bla(CTX-M), bla(TEM), and bla(SHV) resistance genes. Thirty-five resistant isolates were detected, including 26 isolates that contained pAmpC (bla(CMY-2)), and nine ESBL-producing isolates harboring bla(CTX-M) (n = 4, consisting of two bla(CTX-M-2) and two bla(CTX-M-15 genes)), bla(TEM) (n = 4, consisting of one bla(TEM-20) and three bla(TEM-52) genes), and bla(SHV) (n = 1, bla(SHV-12)). All pAmpC-harboring and ESBL-producing Salmonella isolates were obtained from samples collected after 2005, and the percentage of resistant isolates increased significantly from 0% in 2004 to 27.9% in 2010 (P for trend = 0.006). This increase was caused in part by an increase in the number of Salmonella enterica subsp. enterica serovar Infantis strains harboring an approximately 280-kb plasmid containing bla(CMY-2) in proximity to ISEcp1. The dissemination of ESC-resistant Salmonella containing plasmid-mediated bla(CMY-2) in chicken products indicates the need for the development of continuous monitoring strategies in the interests of public health.
Project description:The aim of the present study was to determine the prevalence and to characterize extended-spectrum β-lactamases- and/or carbapenemases-producing Enterobacteriaceae among Enterobacteriaceae isolated from retail chicken meat in Zagazig, Egypt.One hundred and six Enterobacteriaceae isolates were collected from retail chicken meat samples purchased in Zagazig, Egypt in 2013. Species identification was done by MALDI-TOF MS. Screening for ESBL-E was performed by inoculation of isolates recovered from meat samples onto the EbSA (Cepheid Benelux, Apeldoorn, the Netherlands) selective screening agar. ESBL production was confirmed by combination disc diffusion test with clavulanic acid (Rosco, Taastrup, Denmark). Carbapenemases production was confirmed with double disk synergy tests. Resistance genes were characterized by PCR with specific primers for TEM, SHV, and CTX-M and carbapenemases (KPC, NDM, OXA-48, IMP and VIM). PCR products of CTX-M genes were purified and sequenced. Phylogenetic grouping of E. coli was performed by a PCR-based method.Of these 106 isolates 69 (65.09%) were ESBL producers. Twelve (11.32%) of these isolates were also phenotypically class B carbapenemases producer. TEM genes were detected in 61 (57.55%) isolates. 49 (46.23%) isolates harbored CTX-M genes, and 25 (23.58%) carried genes of the SHV family. All CPE belonged to the NDM group. The predominant CTX-M sequence type was CTX-M-15 (89.80%). The majority (80%) of the ESBL-EC belonged to low virulence phylogroups A and B1.This is the first study from Egypt reporting high rates of ESBLs and carbapenemases (65.09% and 11.32%, respectively) in Enterobacteriaceae isolated from retail chicken meat. These results raise serious concerns about public health and food safety as retail meat could serve as a reservoir for these resistant bacteria which could be transferred to humans through the food chain.
Project description:<h4>Background</h4>The CTX-M family of extended-spectrum beta lactamase (ESBL) enzymes is comprised of over 60 <i>bla</i><sub>CTX-M</sub> gene variants with the predominance of <i>bla</i><sub>CTX-M-15</sub> in many regions. In this report, we present the first description of <i>bla</i><sub>CTX-M-28</sub> in the United Arab Emirates.<h4>Methods</h4>Forty-five non-duplicate ESBL producing isolates identified in a secondary care facility in the United Arab Emirates from June to July 2016 were studied. Gene sequencing was performed and DNA sequences were annotated using the BLAST program to identify the gene subtypes.<h4>Results</h4>The majority of the ESBL positive isolates were <i>E. coli</i> (<i>n</i>/<i>N</i> = 39/45; 86.6%) followed by <i>K. pneumoniae</i> (<i>n</i> = 5) and <i>K. oxytoca</i> (<i>n</i> = 1). All isolates harboured <i>bla</i><sub>CTX-M</sub> and <i>bla</i><sub>TEM</sub> genes, 18 had <i>bla</i><sub>SHV</sub>, and 2 were <i>bla</i><sub>VIM</sub> positive. Thirty-seven isolates (82.2%) were positive for <i>bla</i><sub>CTX-M-28</sub>. Other <i>bla</i><sub>CTX-M</sub> genes identified include <i>bla</i><sub>CTX-M-167</sub> (<i>n</i> = 2; isolates #1 and 26) and one each for <i>bla</i><sub>CTX-M-38</sub>, <i>bla</i><sub>CTX-M-163</sub>, and <i>bla</i><sub>CTX-M-198</sub>. No <i>bla</i><sub>CTX-M-15</sub> was identified. The predominant <i>bla</i><sub>TEM</sub> subtype was <i>bla</i><sub>TEM-171</sub> (<i>n</i> = 8) followed by one of each of <i>bla</i><sub>TEM-120</sub>, <i>bla</i><sub>TEM-163</sub>, and <i>bla</i><sub>TEM-206</sub>. The <i>bla</i><sub>SHV</sub> subtypes were <i>bla</i><sub>SHV-148</sub> and <i>bla</i><sub>SHV-187</sub>.<h4>Conclusion</h4>The findings indicate the first description of <i>bla</i><sub>CTX-M-28</sub> in a setting where <i>bla</i><sub>CTX-M-15</sub> was previously predominant.
Project description:Retail beef and pork, including processed products, can serve as vehicles for the zoonotic foodborne transmission of pathogens and antimicrobial resistant bacteria. However, processed and seasoned products like sausages, are not often included in research and surveillance programs. The objective of this study was to investigate retail ground beef and pork, including processed products, for the presence of common foodborne pathogens and antimicrobial resistant bacteria. We purchased 763 packages of fresh and fully cooked retail meat products during 29 visits to 17 grocery stores representing seven major grocery chains located in west and central Ohio. Each package of meat was evaluated for contamination with methicillin-resistant Staphylococcus aureus (MRSA), Salmonella spp., Enterobacteriaceae expressing extended-spectrum cephalosporin resistance, and carbapenemase-producing organisms (CPO). Only 3 of the 144 (2.1%) packages of fully cooked meat products contained any of these organisms, 1 with an extended-spectrum β-lactamase-producing (ESBL) Enterobacteriaceae and 2 with CPO. Among the 619 fresh meat products, we found that 85 (13.7%) packages were contaminated with MRSA, 19 (3.1%) with Salmonella, 136 (22.0%) with Enterobacteriaceae expressing an AmpC (bla<sub>CMY</sub>) resistance genotype, 25 (4.0%) with Enterobacteriaceae expressing an ESBL (bla<sub>CTX-M</sub>) resistance genotype, and 31 (5.0%) with CPO, primarily environmental organisms expressing intrinsic carbapenem resistance. However, one CPO, a Raoultella ornithinolytica, isolated from pork sausage co-harbored both bla<sub>KPC-2</sub> and bla<sub>NDM-5</sub> on IncN and IncX3 plasmids, respectively. Our findings suggest that fresh retail meat, including processed products can be important vehicles for the transmission of foodborne pathogens and antimicrobial resistant bacteria, including those with epidemic carbapenemase-producing genotypes.
Project description:Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae have rapidly spread worldwide and pose a serious threat for health care-associated (HA) infection. We conducted molecular detection and characterization of ESBL-related bla genes, including bla(TEM), bla(SHV), bla(CTX-M), bla(VEB), bla(OXA), bla(PER), and bla(GES), among 362 isolates of ESBL-producing E. coli (n = 235) and ESBL-producing K. pneumoniae (n = 127) collected from patients who met the definition of HA infection at two major university hospitals in Thailand from December 2004 to May 2005. The prevalence of ESBL-producing E. coli and ESBL-producing K. pneumoniae, patient demographics and the susceptibilities of these bacteria to various antimicrobial agents were described. A total of 87.3% of isolates carried several bla genes. The prevalence of bla(CTX-M) was strikingly high: 99.6% for ESBL-producing E. coli (CTX-M-14, -15, -27, -40, and -55) and 99.2% for ESBL-producing K. pneumoniae (CTX-M-3, -14, -15, -27, and -55). ISEcp1 was found in the upstream region of bla(CTX-M) in most isolates. Up to 77.0% and 71.7% of ESBL-producing E. coli and ESBL-producing K. pneumoniae, respectively, carried bla(TEM); all of them encoded TEM-1. ESBL-producing K. pneumoniae carried bla(SHV) at 87.4% (SHV-1, -2a, -11, -12, -27, -71, and -75) but only at 3.8% for ESBL-producing E. coli (SHV-11 and -12). bla genes encoding VEB-1 and OXA-10 were found in both ESBL-producing E. coli (8.5% and 8.1%, respectively) and ESBL-producing K. pneumoniae (10.2% and 11.8%, respectively). None of the isolates were positive for bla(PER) and bla(GES). Pulsed-field gel electrophoresis analysis demonstrated that there was no major clonal relationship among these ESBL producers. This is the first study to report CTX-M-3, CTX-M-27, CTX-M-40, SHV-27, SHV-71, and SHV-75 in Thailand and to show that CTX-M ESBL is highly endemic in the country.