Epidemiological Study on Prevalence, Serovar Diversity, Multidrug Resistance, and CTX-M-Type Extended-Spectrum ?-Lactamases of Salmonella spp. from Patients with Diarrhea, Food of Animal Origin, and Pets in Several Provinces of China.
ABSTRACT: A total of 2,283 Salmonella 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 Salmonella spp. was detected in chicken meats (39.3%, 486/1,237). Fifteen serogroups and 66 serovars were identified, with Salmonella enterica 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 blaCTX-M genes were identified, with blaCTX-M-65, blaCTX-M-123, blaCTX-M-14, blaCTX-M-79, and blaCTX-M-130 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 oqxA, oqxB, qepA, qnrB, and qnrS 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 Salmonella 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 Salmonella isolates.
Project description:<h4>Background</h4>The prevalence of extended-spectrum ?-lactamases (ESBLs) have been reported in clinical isolates obtained from various hospitals in Ethiopia. However, there is no data on the prevalence and antibiotic susceptibility patterns of CTX-M type ESBL produced by Gram-negative bacilli. The aim of this study was to determine the frequency and distribution of the bla<sub>CTX-M</sub> genes and the susceptibility patterns in ESBL producing clinical isolates of Gram-negative bacilli in Jimma University Specialized Hospital (JUSH), southwest Ethiopia.<h4>Methods</h4>A total of 224 non-duplicate and pure isolates obtained from clinically apparent infections, were included in the study. Identification of the isolates was performed by MALDI-TOF mass spectrometry. Susceptibility testing and ESBL detection was performed using VITEK® 2, according to EUCAST v4.0 guidelines. Genotypic analysis was performed using Check-MDR CT103 Microarrays.<h4>Results</h4>Of the total 112 (50.0%) isolates screen positive for ESBLs, 63.4% (71/112) tested positive for ESBL encoding genes by Check-MDR array, which corresponds to 91.8% (67/73) of the total Enterobacteriaceae and 10.3% (4/39) of nonfermenting Gram-negative bacilli. Among the total ESBL gene positive isolates, 95.8% (68/71) carried bla<sub>CTX-M</sub> genes with CTX-M group 1 type15 being predominant (66/68; 97.1% of CTX-M genes). The bla<sub>CTX-M</sub> carrying Enterobacteriaceae (n =?64) isolates showed no resistance against imipenem and meropenem and a moderate resistance rate against tigecycline (14.1%), fosfomycin (10.9%) and amikacin (1.6%) suggesting the effectiveness of these antibiotics against most isolates. On the other hand, all the bla<sub>CTX-M</sub> positive Enterobacteriaceae showed a multidrug resistant (MDR) phenotype with remarkable co-resistances (non-susceptibility rates) to aminoglycosides (92.2%), fluoroquinolones (78.1%) and trimethoprim/sulfamethoxazol (92.2%).<h4>Conclusions</h4>This study demonstrates a remarkably high prevalence of bla<sub>CTX-M</sub> genes among ESBL-producing isolates. The high level of resistance to ?-lactam and non-?-lactam antibiotics as well as the trend to a MDR profile associated with the bla<sub>CTX-M</sub> genes are alarming and emphasize the need for routine diagnostic antimicrobial susceptibility testing for appropriate choice of antimicrobial therapy.
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: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 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:<h4>Background</h4>The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. bla<sub>CTX-M</sub> genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that bla<sub>CTX-M</sub>-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated bla<sub>CTX-M</sub> and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements.<h4>Methods</h4>A total of 46 clinical isolates of cefotaxime-resistant Enterobacteriaceae (1 Enterobacter cloacae, 9 Klebsiella pneumoniae, and 36 Escherichia coli) from Zambia were subjected to whole-genome sequencing (WGS) using MiSeq and MinION. By reconstructing nearly complete genomes, bla<sub>CTX-M</sub> genes were categorized as either chromosomal or plasmid-borne.<h4>Results</h4>WGS-based genotyping identified 58 AMR genes, including four bla<sub>CTX-M</sub> alleles (i.e., bla<sub>CTX-M-14</sub>, bla<sub>CTX-M-15</sub>, bla<sub>CTX-M-27</sub>, and bla<sub>CTX-M-55</sub>). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination of bla<sub>CTX-M</sub> genes. Out of 45 bla<sub>CTX-M</sub> gene-carrying strains, 7 harbored the gene in their chromosome. In one E. cloacae and three E. coli strains, chromosomal bla<sub>CTX-M-15</sub> was located on insertions longer than 10 kb. These insertions were bounded by ISEcp1 at one end, exhibited a high degree of nucleotide sequence homology with previously reported plasmids, and carried multiple AMR genes that corresponded with phenotypic AMR profiles.<h4>Conclusion</h4>Our study revealed the co-occurrence of ISEcp1-bla<sub>CTX-M-15</sub> and multiple AMR genes on chromosomal insertions in E. cloacae and E. coli, suggesting that ISEcp1 may be responsible for the transposition of diverse AMR genes from plasmids to chromosomes. Stable retention of such insertions in chromosomes may facilitate the successful propagation of MDR clones among these Enterobacteriaceae species.
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:Nontyphoidal Salmonella (NTS) is one of the most prevalent bacterial causes of gastrointestinal infections worldwide. Meanwhile, the detection rate of CTX-M-55 ESBL-positive has increased gradually in China. To identify the molecular epidemiological and genomic characteristics of <i>bla</i><sub>CTX-M-55</sub>-carrying nontyphoidal Salmonella (NTS) clinical isolates, a total of 105 NTS isolates were collected from a Chinese tertiary hospital. Antimicrobial susceptibility testing was performed to determine the resistance phenotype. Whole-genome sequencing and bioinformatics analysis were used to determine the antimicrobial resistance genes, serotypes, phylogenetic relationships, and the genetic environment of the <i>bla</i><sub>CTX-M-55</sub> gene. The results showed that among the 22 ceftriaxone resistant isolates, the <i>bla</i><sub>CTX-M-55</sub> was the most common β-Lactamase gene carried by 14 isolates, including serotypes <i>S.</i> Typhimurium (10/14), <i>S.</i> Muenster (2/14), <i>S.</i> Rissen (1/14), and <i>S.</i> Saintpaul (1/14). Phylogenetic analysis shows that 10 <i>bla</i><sub>CTX-M-55</sub>-positive <i>S.</i> Typhimurium ST34 isolates were divided into two clusters. The genetic relationship of isolates in each cluster was very close (≤10 cgMLST loci). The <i>bla</i><sub>CTX-M-55</sub> gene was located on the chromosome in 10 isolates, on IncI1 plasmid in three isolates, and IncHI2 plasmid in one isolate. In conclusion, the <i>bla</i><sub>CTX-M-55</sub> gene, mainly located on the chromosome of <i>S.</i> Typhimurium ST34 isolates, was the main driving force associated with the resistance of NTS to cephalosporins. Therefore, close attention to the clonal dissemination of <i>bla</i><sub>CTX-M-55</sub>-carrying <i>S.</i> Typhimurium ST34 in clinical settings must be monitored carefully. <b>IMPORTANCE</b> ESCs are the first choice for treating NTS infections. However, ESBLs and AmpC β-lactamases are the most typical cause for ESCs resistance. The CTX-M-55 ESBL-positive rate has gradually increased in the clinic in recent years. At present, the research about <i>bla</i><sub>CTX-M-55</sub>-positive Salmonella mainly focuses on the foodborne animals or the environment while less on clinical patients. Thus, this study was carried out for identifying molecular epidemiological and genomic characteristics of <i>bla</i><sub>CTX-M-55</sub>-carrying NTS clinical isolates. The results showed that the <i>bla</i><sub>CTX-M-55</sub> gene, mainly located on the chromosome of <i>S.</i> Typhimurium ST34 isolates from Conghua District, was the main driving force associated with the resistance of NTS to cephalosporins. Therefore, our work highlights the importance of monitoring the clonal dissemination of <i>bla</i><sub>CTX-M-55</sub>-carrying <i>S.</i> Typhimurium ST34 in clinical settings.
Project description:The non-Typhi <i>Salmonella</i> (NTS) infection is critical to children's health, and the ceftriaxone is the important empirical treatment choice. With the increase resistance rate of ceftriaxone in <i>Salmonella</i>, the molecular epidemiology and resistance mechanism of ceftriaxone-resistant <i>Salmonella</i> needs to be studied. From July 2019 to July 2020, a total of 205 NTS isolates were collected, 195 of which (95.1%) were cultured from stool, but 10 isolates were isolated from an extraintestinal site. Serogroup B accounted for the vast majority (137/205) among the isolates. Fifty-three isolates were resistant to ceftriaxone, and 50 were isolated from children younger than 4years of age. The resistance rates for ceftriaxone, ciprofloxacin, and levofloxacin were significantly higher in younger children than the older children. The resistance genes in the ceftriaxone-susceptible isolates were detected by PCR, and ceftriaxone-resistant <i>Salmonella</i> were selected for further whole-genome sequencing. Whole-genome analysis showed that serotype Typhimurium and its monophasic variant was the most prevalent in ceftriaxone-resistant isolates (37/53), which comprised ST34 (33/53), ST19 (2/53), and ST99 (2/53), and they were close related in the phylogenetic tree. However, the other isolates were diverse, which included one Enteritidis (ST11), one Indiana (ST17), one Derby (ST40), four Kentucky (ST198), two Goldcoast (ST2529, ST358), one Muenster (ST321), one Virchow (ST359), one Rissen (ST469), one Kedougou (ST1543), two Uganda (ST684), and one Kottbus (ST8839). Moreover, CTX-M-55 ESBLs production (33/53) was found to be mainly responsible for ceftriaxone resistance, followed by <i>bla</i> <sub>CTX-M-65</sub> (12/53), <i>bla</i> <sub>CTX-M-14</sub> (4/53), <i>bla</i> <sub>CTX-M-9</sub> (2/53), <i>bla</i> <sub>CTX-M-64</sub> (1/53), <i>bla</i> <sub>CTX-M-130</sub> (1/53), and <i>bla</i> <sub>CMY-2</sub> (1/53). IS<i>Ecp1</i>, IS<i>903B</i>, IS <i>Kpn26</i>, IS<i>1F</i>, and IS<i>26</i> were connected to antimicrobial resistance genes transfer. In conclusion, the dissemination of ESBL-producing <i>Salmonella</i> isolates resulted in an increased prevalence of ceftriaxone resistance in young children. The high rate of multidrug resistance should be given additional attention.
Project description:The objective of this study was to analyse the mechanisms of resistance to carbapenems and other extended-spectrum-β-lactams and to determine the genetic relatedness of multidrug-resistant Enterobacterales (MDR-E) causing colonization or infection in solid-organ transplantation (SOT) recipients. Prospective cohort study in kidney (n = 142), liver (n = 98) or kidney/pancreas (n = 7) transplant recipients between 2014 and 2018 in seven Spanish hospitals. We included 531 MDR-E isolates from rectal swabs obtained before transplantation and weekly for 4-6 weeks after the procedure and 10 MDR-E from clinical samples related to an infection. Overall, 46.2% Escherichia coli, 35.3% Klebsiella pneumoniae, 6.5% Enterobacter cloacae, 6.3% Citrobacter freundii and 5.7% other species were isolated. The number of patients with MDR-E colonization post-transplantation (176; 71.3%) was 2.5-fold the number of patients colonized pre-transplantation (71; 28.7%). Extended-spectrum β-lactamases (ESBLs) and carbapenemases were detected in 78.0% and 21.1% of MDR-E isolates respectively. In nine of the 247 (3.6%) transplant patients, the microorganism causing an infection was the same strain previously cultured from surveillance rectal swabs. In our study we have observed a low rate of MDR-E infection in colonized patients 4-6 weeks post-transplantation. E. coli producing bla<sub>CTX-M-G1</sub> and K. pneumoniae harbouring bla<sub>OXA-48</sub> alone or with bla<sub>CTX-M-G1</sub> were the most prevalent MDR-E colonization strains in SOT recipients.
Project description:BACKGROUND: Commensal Escherichia coli are a prominent reservoir of genes coding for antibiotic resistance and also responsible for endogenous infections in pregnant women. We studied the factors in pregnant women associated with carriage of multi-drug resistant (MDR) E. coli and genetic determinants of antibiotic resistance in them. METHODS: Women attending to Obstetric and Gynaecology department outpatient clinics for routine antenatal check-up were administered a questionnaire. Peri-anal swabs were collected for culture isolation and identification of E.coil. Antibiotic sensitivity was done using the Kirby-Bauer disc diffusion method as recommended by the CLSI guidelines. MICs for quinolones and third generation cephalosporins were done using the agar dilution method. Genes coding for production of beta lactamses and for the quinolone resistance determinant were screened by polymerase chain reaction. Rep-PCR was done on MDR isolates for detecting possible genetic similarity. Multiple logistic regression models were used to determine the independent factors associated with carriage of MDR isolates. RESULTS: A total of 710 isolates of E. coli from 710 women (mean age 26 years) were included in the study. Resistance to at least one antibiotic tested was detected in 94% of the E. coli isolates. A total of 109 isolates were ESBL producing and 35 isolates were MDR. In the MDR isolates MIC(50) and MIC(90) for quinolones and third generation cephalosporins were high for those isolates that carried bla(TEM) gene (26 isolates) and bla(CTX-M) gene (24 isolates). Both bla(TEM) and bla(CTX-M) genes were detected in 19 isolates. The commonest Plasmid Mediated Quinolone Resistance (PMQR) gene identified was aac(6')-Ib-cr (n?=?23/25). All isolates carrying the PMQR genes were also positive for bla(CTX-M) and bla(TEM) gene. Mutations in gyr A and par C genes were present in all 35 MDR isolates. The statistically significant risk factors for carriage of MDR E. coli were graduate or post-graduate education, a self-employed status, a family size of more than 10 members, antibiotic usage in last four weeks, and history of hospitalization in the last four weeks. CONCLUSIONS: The presence of genes coding for extended spectrum of beta lactamases and plasmid mediated quinolone resistance in commensal E. coli is disconcerting. The study provides strong basis good antibiotic stewardship.