Characterization of the first extended-spectrum beta-lactamase-producing Salmonella isolate identified in Canada

Serotype Occurrence, Virulence Profiles, Antimicrobial Resistance and Molecular Characterization of Salmonella Isolated from Hospitalized Patients with Gastroenteritis in Great Tunisia between 2010 and 2020

Non-typhoid Salmonella is one of the major causes of food-borne infections worldwide. The aim of the current study is to determine the serotype occurrence, virulence factors and antimicrobial resistance patterns of Salmonella isolated from hospitalized patients. The identification of Salmonella strains was performed according to REMIC, 2018. The susceptibility of Salmonella isolates was assessed against 20 antimicrobials using the disk diffusion method. Some virulence and antimicrobial resistance genes were identified using PCR. Among the 61 isolated Salmonella strains, seven serotypes were identified and all were positive for the virulence genes invA, mgtC and sirA. Critical resistance rates (>40%) were detected for tetracycline, nalidixic acid, amoxicillin and fluoroquinolones. However, resistances to ertapenem, ceftazidim, aztreonam and colistin were null. In addition, 33% of the isolated strains were multidrug-resistant (MDR). Moreover, 80% and 60% of S. Kentucky isolates were identified as fluoroquinolone-resistant and MDR strains, respectively. The qnrB gene was amplified in 63.2% of fluoroquinolone-resistant strains. The dfrA1 gene was identified in 20% (4/20) of the trimethoprim-sulfamethoxazole resistant strains and the integrase Class 2 gene was amplified in only 8.2% (5/61) of the isolates. Our findings highlight the emergence of MDR Salmonella isolates. A rationalization of antimicrobial use is urgently recommended in both human and veterinary medicine.

Characterization of Escherichia coli and Other Enterobacterales Resistant to Extended-Spectrum Cephalosporins Isolated from Dairy Manure in Ontario, Canada

Extended-spectrum cephalosporins (ESCs) resistance genes, such as bla_CTX-M, bla_CMY, and bla_SHV, have been found regularly in bacteria from livestock. However, information on their distribution in dairy cattle in Canada and on the associated genome sequences of ESC-resistant Enterobacterales is sparse. In this study, the diversity and distribution of ESC-resistant Escherichia coli throughout manure treatments in six farms in Southern Ontario were assessed over a one-year period, and their ESC-resistance plasmids were characterized. The manure samples were enriched using selective media. The resulting isolates were screened via polymerase chain reaction for bla_CTX-M, bla_CMY, and bla_SHV. No E. coli carrying bla_SHV were detected. Escherichia coli (n = 248) carrying bla_CTX-M or bla_CMY underwent whole-genome sequencing using an Illumina MiSeq/NextSeq. These isolates were typed using multilocus sequence typing (MLST) and their resistance gene profiles. A subset of E. coli (n = 28) were sequenced using Oxford Nanopore Technologies. Plasmids were assembled using Unicycler and characterized via the resistance genes pattern, replicon type, plasmid MLST, phylogenetic analysis, and Mauve alignments. The recovery of ESC-resistant Enterobacterales (18 species, 8 genera) was drastically reduced in manure outputs. However, multiple treatment stages were needed to attain a significant reduction. 62 sequence types were identified, with ST10, ST46, ST58, ST155, ST190, ST398, ST685, and ST8761 being detected throughout the treatment pipeline. These STs overlapped with those found on multiple farms. The ESC-resistance determinants included CTX-M-1, -14, -15, -17, -24, -32, -55, and CMY-2. The plasmids carrying bla_CTX-M were more diverse than were the plasmids carrying bla_CMY. Known "epidemic plasmids" were detected for both bla_CTX-M and bla_CMY. IMPORTANCE The increase in antimicrobial resistance is of concern for human and animal health, especially when resistance is conferred to extended-spectrum cephalosporins, which are used to treat serious infections in both human and veterinary medicine. Bacteria carrying extended-spectrum cephalosporin resistance genes, including bla_CTX-M and bla_CMY, are frequently found in dairy manure. Manure treatment influences the loads and diversity of bacteria, including those carrying antimicrobial resistance genes, such as Enterobacterales and Escherichia coli. Any bacteria that survive the treatment process are subsequently applied to the environment. Enterobacterales carrying bla_CTX-M or bla_CMY can contaminate soil and crops consumed by humans and animals, thereby increasing the potential for antimicrobial resistance genes to integrate into the human gut microflora through horizontal gene transfer. This furthers the dissemination of resistance. Therefore, it is imperative to understand the effects manure treatments have on ESC-resistance in environmentally applied manure.

Genetic Diversity and New Sequence Types of Escherichia coli Coharboring β-Lactamases and PMQR Genes Isolated from Domestic Dogs in Central Panama

Background: β-lactamase-producing Escherichia coli are a widely distributed source of antimicrobial resistance for animals and humans. Little is known about the susceptibility profile and genetic characteristics of E. coli strains isolated from domestic dogs in Latin America. Methods: We report on a cross-sectional study that evaluated E. coli strains isolated from fecal samples of domestic dogs in central Panama. The extended-spectrum β-lactamase (ESBL), AmpC genes, and plasmid-mediated quinolone resistance were investigated. Molecular typing using Pasteur’s multilocus sequence typing (MLST) was conducted. Results: A total of 40 E. coli isolates were obtained, of which 80% (32/40) were resistant to at least one of the antibiotics tested, while 20% (8/40) were sensitive to all antibiotics analyzed in this study (p < 0.001). Forty percent of the strains were resistant to three or more antibiotics. The most common resistance was to tetracycline (45%) and ampicillin (30%) while 2.5% showed an ESBL phenotype. Antibiotic resistance genes were detected for one β-lactamase (blaTEM-1) and two plasmid-mediated quinolone resistance (PMQR) enzymes (qnrS and qnrB). In addition, mutations in the chromosomal AmpC gene were observed at positions −35, −28, −18, −1, and +58. Fourteen different sequence types (STs) were identified; the most frequent were ST399 and ST425 (12% each). ST3 and ST88, which have been previously identified in human clinical isolates, were also evidenced. Three new STs were found for the first time: ST1015, ST1016 (carrier of the blaTEM-1 gene), and ST1017 (carrier of the blaTEM-1, qnrS, and qnrB genes). Conclusions: In the intestinal strains of E. coli isolated from domestic dogs, there was a high frequency of resistance to antibiotics. The presence of genes from plasmids and chromosomal mutations that conferred antibiotic resistance, the identification of isolates previously reported in humans, and the genetic diversity of STs (including three that were newly identified) confirmed the determinants of resistance to antibiotics in the domestic dogs from central Panama.

Salmonella Broiler Meat's Contamination in Tunisia: Prevalence, Serotypes, Antimicrobial Resistance and Molecular Characterization of Isolated Strains

This study was conducted in north-eastern Tunisia to estimate the contamination prevalence of Salmonella in broilers' meat, to rank serotypes and to characterize the isolated multidrug-resistant (MDR) strains. A total number of 1288 meat samples were collected from 322 broiler batches; Salmonella isolates were identified by the alternative technique VIDAS Easy Salmonella. The susceptibility of Salmonella isolates was assessed against 21 antimicrobials using the disc diffusion method on Mueller-Hinton agar. Some antimicrobial resistance genes were identified using Polymerase Chain Reaction (PCR). The prevalence rates of Salmonella in the neck skin and the breast muscle contamination were estimated at 11.8% (38/322) and 0.9% (3/322), respectively. The prevalence rate of Salmonella in meat cutting parts contamination was estimated at 5.1% (33/644). Eight serotypes of Salmonella were identified, namely S. Enteritidis, S. Kentucky, S. Anatum, S. Infantis, S. Mbandaka, S. Zanzibar, S. Hadar and S. Agona. High rate of resistance was identified against amoxicillin (91.9%), nalidixic acid (83.8%), tetracycline (75.7%), streptomycin (73%), ciprofloxacin (70%), sulfamides (68.9%), cefalotin (68.9%), cefotaxim (67.6%) and cefoxitin (60.8%). The majority (90.5%; 67/74) of isolated strains was recognized as MDR. Nine MDR strains were identified as Extended-Spectrum β-Lactamase (ESBL) producers. The bla_CTX-M gene was identified by PCR in all the nine ESBL strains. TetA, tetB and dfrA1 genes were amplified in 3.6% (2/56), 1.8% (1/56) and 19.3% (5/26) of tetracycline and trimethoprim-resistant strains, respectively. The integrase gene (class 2) was identified in only 8.1% (6/74) of the Salmonella-isolated strains. Our findings highlight the emergence of MDR Salmonella isolates in Tunisia.

Prevalence of extended-spectrum β-lactamase-producing Enterobacterales in retail sheep meat from Zagazig city, Egypt

Background

The goal of this study was to investigate the prevalence of extended-spectrum β-lactamase production in Enterobacterales isolated from retail sheep meat in Zagazig, Egypt.

Methods

One hundred random samples of sheep meat were collected from different retail butcher shops (n = 5) in the city of Zagazig, Egypt. Bacterial isolates were identified by MALDI-TOF MS and screened for antibiotic susceptibility by disk diffusion; further genotypic characterization of β-lactamase-encoding genes was performed with Real-Time PCR. E. coli strains were phylotyped with the Clermont triplex PCR method.

Results

Of the total of 101 bacterial isolates recovered from retail sheep meat samples, 93 were E. coli, six were Enterobacter cloacae and two were Proteus mirabilis. As many as 17% of these 100 samples showed ESBL phenotypes, all were E. coli. The bla_CTX-M genes were detected in seven isolates (six were bla_CTX-M-15 and one was bla_CTX-M-14), three isolates harboured bla_TEM (all were bla_TEM-one), and two carried genes of the bla_SHV family (both were bla_SHV-12). Eight E. coli isolates expressed ESBL phenotype but no bla_TEM, bla_SHV or bla_CTX-M genes were detected by PCR. ESBL- positive E. coli isolates were nearly equally distributed over the commensal groups A/B1 and the virulent group D.

Conclusion

Nearly one in five sheep meat samples was contaminated with ESBL-E. coli. This further corroborates the potential role played by contaminated meat in the increasing resistance rates that have been reported worldwide.

Diversity of blaCTX-M-1-carrying plasmids recovered from Escherichia coli isolated from Canadian domestic animals

Conserved IncI1 and IncHI1 plasmids carrying blaCTX-M-1 have been found circulating in chickens and horses from continental Europe, respectively. In Canada, blaCTX-M-1 is overwhelmingly the most common blaCTX-M variant found in Escherichia coli from chicken and horses and can be recovered at lower frequencies in swine, cattle, and dogs. Whole-genome sequencing has identified a large genetic diversity of isolates carrying this variant, warranting further investigations into the plasmids carrying this gene. Therefore, the objective of this study was to describe the genetic profiles of blaCTX-M-1 plasmids circulating in E. coli from Canadian domestic animals and compare them to those recovered in animals in Europe. Fifty-one blaCTX-M-1 positive E. coli isolates from chicken (n = 14), horses (racetrack horses n = 11; community horses n = 3), swine (n = 7), turkey (n = 6), dogs (n = 5), beef cattle (n = 3), and dairy cattle (n = 2) were selected for plasmid characterization. Sequences were obtained through both Illumina and Oxford Nanopore technologies. Genomes were assembled using either Unicycler hybrid assembly or Flye with polishing performed using Pilon. blaCTX-M-1 was found residing on a plasmid in 45 isolates and chromosomally located in six isolates. A conserved IncI1/ST3 plasmid was identified among chicken (n = 12), turkey (n = 4), swine (n = 6), dog (n = 2), and beef cattle (n = 2) isolates. When compared against publicly available data, these plasmids showed a high degree of similarity to those identified in isolates from poultry and swine in Europe. These results suggest that an epidemic IncI1/ST3 plasmid similar to the one found in Europe is contributing to the spread of blaCTX-M-1 in Canada. A conserved IncHI1/FIA(HI1)/ST2 plasmid was also recovered from nearly all racetrack horse isolates (n = 10). Although IncHI1/ST2 plasmids have been reported among European horse isolates, IncHI1/ST9 plasmids appear to be more widespread. Further studies are necessary to understand the factors contributing to these plasmids' success in their respective populations.

Detection of mcr-1 Gene in Undefined Vibrio Species Isolated from Clams

The increase of antimicrobial resistant strains is leading to an emerging threat to public health. Pathogenic Vibrio are responsible for human and animal illness. The Enterobacteriaceae family includes microorganisms that affect humans, causing several infections. One of the main causes of human infection is related to the ingestion of undercooked seafood. Due to their filter-feeding habit, marine invertebrates, such as clams, are known to be a natural reservoir of specific microbial communities. In the present study, Vibrionaceae and coliforms microorganisms were isolated from clams. A microbial susceptibility test was performed using the disk diffusion method. From 43 presumptive Vibrio spp. and 17 coliforms, three Vibrio spp. with MICs to colistin >512 mg L−1 were found. From the 23 antimicrobial resistance genes investigated, only the three isolates that showed phenotypic resistance to colistin contained the mcr-1 gene. Genotypic analysis for virulence genes in EB07V indicated chiA gene presence. The results from the plasmid cure and transformation showed that the resistance is chromosomally mediated. Biochemical analysis and MLSA, on the basis of four protein-coding gene sequences (recA, rpoB, groEL and dnaJ), grouped the isolates into the genus Vibrio but distinguished them as different from any known Vibrio spp.

Prevalence, Risk Factors, Antimicrobial Resistance and Molecular Characterization of Salmonella in Northeast Tunisia Broiler Flocks

This study was conducted in northeastern Tunisia to estimate both the prevalence and the risk factors of Salmonella in broiler flocks as well as to characterize the isolated multidrug-resistant (MDR) Salmonella strains. In the present study, a total number of 124 farms were sampled; Salmonella isolates were identified by the alternative technique VIDAS Easy Salmonella. The susceptibility of Salmonella isolates was assessed against 21 antimicrobials using the disk diffusion method on Mueller–Hinton agar using antimicrobial discs. Some antimicrobial resistance genes were identified using PCR. The prevalence rate of Salmonella infection, in the sampled farms, was estimated at 19.9% (64/322). Moreover, a total number of 13 different serotypes were identified. High rate of resistance was identified against nalidixic acid (82.85%), amoxicillin (81.25%), streptomycin (75%), and ciprofloxacin (75%). Alarming level of resistance to ertapenem (12.5%) was noticed. A total of 87.5% (56/64) of isolated strains were recognized as MDR. Three MDR strains were extended-spectrum β-lactamases (ESBL)-producers and three MDR strains were cephalosporinase-producers. The bla_CTX-M gene was amplified in all the three ESBL strains. The qnrB gene was not amplified in fluoroquinolones-resistant strains. The tetA and tetB genes were amplified in 5% (2/40) and 2.5% (1/40) of tetracycline-resistant strains, respectively. The dfrA1 gene was amplified in five of the 20 trimethoprim-resistant strains. The mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5 genes were not amplified in any of the phenotypically colistin-resistant strains. In terms of integrase genes int1 and int2, only gene class 2 was amplified in 11% (7/64) of analyzed strains. Risk factors, such as the poor level of cleaning and disinfection, the lack of antimicrobial treatment at the start of the breeding, and a crawl space duration lower than 15 days, were associated with high Salmonella infection in birds. These data should be considered when preparing salmonellosis control programs in Tunisian broiler flocks.

Detection of carbapenem-resistance genes in bacteria isolated from wastewater in Ontario

Bacterial carbapenem resistance is a major public health concern since these antimicrobials are often the last resort to treat serious human infections. To evaluate methodologies for detection of carbapenem resistance, carbapenem-tolerant bacteria were isolated from wastewater treatment plants in Toronto, Ottawa, and Arnprior, Ontario. A total of 135 carbapenem-tolerant bacteria were recovered. Polymerase chain reaction (PCR) indicated the presence of carbapenem hydrolysing enzymes KPC ( n = 10), GES ( n = 5), VIM ( n = 7), and IMP ( n = 1), and β-lactamases TEM ( n = 7), PER ( n = 1), and OXA-variants ( n = 16). A subset of 46 isolates were sequenced and analysed using ResFinder and CARD-RGI. Both programs detected carbapenem resistance genes in 35 sequenced isolates and antimicrobial resistance genes (ARGs) conferring resistance to multiple class of other antibiotics. Where β-lactamase resistance genes were not initially identified, lowering the thresholds for ARG detection enabled identification of closely related β-lactamases. However, no known carbapenem resistance genes were found in seven sequenced Pseudomonas spp. isolates. Also of note was a multi-drug-resistant Klebsiella pneumoniae isolate from Ottawa, which harboured resistance to seven antimicrobial classes including β-lactams. These results highlight the diversity of genes encoding carbapenem resistance in Ontario and the utility of whole genome sequencing over PCR for ARG detection where resistance may result from an assortment of genes.

Isolation and molecular characterization of multidrug-resistant Escherichia coli from chicken meat

Antibiotic-resistant Escherichia coli (E. coli) are common in retail poultry products. In this study, we aimed to isolate and characterize multidrug resistant (MDR) E. coli in raw chicken meat samples collected from poultry shops in Sylhet division, Bangladesh, as well as to determine correlation between resistance phenotype and genotype. A total of 600 chicken meat swabs (divided equally between broiler and layer farms, n = 300 each) were collected and the isolates identified as E. coli (n = 381) were selected. Disc diffusion antimicrobial susceptibility assay showed resistance of these isolates to ampicillin, erythromycin, tetracycline, streptomycin, trimethoprim-sulfamethoxazole, chloramphenicol, and gentamicin. Polymerase chain reaction (PCR) identified several antibiotic resistance genes (ARGs) in our isolates. Among these ARGs, the prevalence of tetA (for tetracycline) was the highest (72.58%) in broiler chicken isolates, followed by sul1 (for sulfonamide; 44.16%), aadA1 (for streptomycin; 33.50%), ereA (for erythromycin; 27.41%), aac-3-IV (for gentamicin; 25.38%), and the two genes cmlA (24.87%) and catA1 (8.63%) for chloramphenicol. On the other hand, the respective prevalence in layer chicken isolates were 82.06%, 47.83%, 35.87%, 35.33%, 23.91%, 19.02%, and 5.43%. Furthermore, 49.23% of the isolates from broiler chicken were MDR, with the presence of multiple antibiotic resistance genes, including 3 (40.11%) and 4 (9.13%) genes. On the other hand, 51.09% of layer chicken E. coli isolates were MDR, with 3, 4 or 5 ARGs detected in 36.41%, 14.13%, and 0.54% of the isolates, respectively. We also found that 12.8% of broiler chicken E. coli isolates and 7.61% of layer chicken isolates carried genes coding for extended-spectrum SHV beta-lactamases. Lastly, we report the presence of the AmpC beta-lactamase producing gene (CITM) in 4.56% and 3.26% of broiler and layer chicken E. coli isolates, respectively. We found significant correlations between most of the antimicrobial resistant phenotypes and genotypes observed among the investigated E. coli isolates. Our findings highlight the need for the prudent use of antimicrobials in chickens to minimize the development of antibiotic-resistant bacterial strains.

Molecular characteristics of the new emerging global clone ST1193 among clinical isolates of Escherichia coli from neonatal invasive infections in China

Sequence type 1193 (ST1193) constitutes an emerging fluoroquinolone-resistant Escherichia coli clone in several countries. However, reports of such isolates in neonatal invasive diseases are limited. Here, we assessed the antimicrobial resistance and molecular characteristics of E. coli ST1193 isolates causing neonatal bloodstream infections and meningitis in China. A total of 56 E. coli isolates were collected from neonatal blood and cerebrospinal fluid between September 2009 and June 2015. Antimicrobial susceptibility was evaluated using E-test methods. Polymerase chain reaction amplification was used to detect antibiotic resistance genes including bla_TEM, bla_SHV, and bla_CTX-M groups. Molecular typing was performed via multi-locus sequence typing. Among 56 E. coli isolates, 17 (17/56, 30.4%) were extended-spectrum β-lactamase (ESBL) producers, and 37(37/56, 66.1%) were multidrug-resistant. The most frequent sequence types were ST1193 (12/56), followed by ST95 and ST62. ST1193 isolates exhibited a 91.7% resistance rate to ciprofloxacin, amoxicillin, and sulfonamides, and 83.3% resistance rate to tetracycline. A total of 4 (33.3%) among the 12 ST1193 isolates were ESBL producers, of which three carried both bla_CTX-M-15 and bla_TEM genes with the remaining isolate harboring bla_CTX-M-27 and bla_TEM genes. Additionally, 1 of the 3 ST1193 isolates obtained from cerebrospinal fluid was an ESBL producer that carried both bla_CTX-M-₁₅ and bla_TEM genes. This study revealed for the first time the molecular characteristics of E. coli ST1193 causing neonatal invasive diseases in China. Notably, we found that ST1193 isolates were multidrug-resistant. Further multicenter studies are needed to assess the molecular epidemiology of ST1193 in China to control its spread.

A review on the origin of multidrug-resistant Salmonella and perspective of tailored phoP gene towards avirulence

Salmonellosis continues to remain a health problem as the causative organism Salmonella spp. developed resistance to many of the antibiotics. As per World Health Organization (WHO), it is estimated that enteric fever, accounts for almost 16 million cases annually and over 600,000 deaths worldwide. Recent data revealed that the multi-drug resistance (MDR) rate of enteric fever was as high as 70% in Asian countries, as compared with the overall reported incidence of 50%. Emergence of MDR typhoid fever demands the use of newer antibiotics which also not offer promising effect in recent days. Effective antimicrobial therapy is required to control morbidity and prevent death from typhoid fever. The studies on PhoP/Q regulation revealed it as a best-characterized transcriptional regulation; a two-component system required for Salmonella pathogenesis which controls the expression of more than 40 genes. The PhoP DNA binding proteins possess positively charged amino acids such as arginine, lysine and histidine which present in the DNA binding site. Prevention of PhoP binding in phoP box may ultimately prevent the expression of many regulatory mechanism which plays vital role in Salmonella virulence. Deepness study of PhoP protein and various mutation swots may offer effectual controlling of MDR Salmonella.

Phenotypic and Genotypic Characterization of Virulence Factors and Susceptibility to Antibiotics in Salmonella Infantis Strains Isolated from Chicken Meat: First Findings in Chile

Simple Summary

Salmonella Infantis (S. Infantis) is a zoonotic pathogen that causes gastroenteritis in humans and animals, with poultry being its main reservoir. This pathogen has emerged over the last few decades in different countries, causing outbreaks in humans subsequent to foodborne transmission. It is important to be able to characterize this pathogen in order to establish control measures in the poultry industry. In this study, we investigated the presence of virulence genes, biofilm formation abilities, antibiotic resistance genes, and antibiotic susceptibility in S. Infantis. The results showed that the S. Infantis strains isolated from chicken meat for sale in supermarkets in Santiago, Chile are multidrug-resistant (MDR) and contain virulence genes, making them pathogenic. Thus, Salmonella Infantis should be under surveillance in the poultry food production chain with the aim of protecting public health.

Abstract

Salmonella Infantis is a zoonotic pathogen that causes gastroenteritis in humans and animals, with poultry being its main reservoir. In Chile, there are no data to characterize S. Infantis strains in poultry production. In this study, 87 S. Infantis strains were isolated from chicken meat for sale in supermarkets in Santiago, Chile, and characterized according to their virulence genes, biofilm formation abilities, antibiotic susceptibility, and resistance genes. Through polymerase chain reaction or PCR, the strains were analyzed to detect the presence of 11 virulence genes, 12 antibiotic resistance genes, and integrase genes. Moreover, disc diffusion susceptibility to 18 antimicrobials and the ability to form biofilm in vitro were evaluated. Results demonstrated six different virulence gene profiles. Ninety-four percent of the strains were multi-resistant to antibiotics with weak biofilm formation abilities, 63.2% of the strains were broad spectrum β- lactam resistant, and the bla_CTX-M-65 gene was amplified in 13 strains. Only 3.4% of the strains were fluoroquinolone resistant, and the qnrB gene was amplified in two strains. Colistin resistance was exhibited in 28.7% of the strains, but mrc genes were not amplified in any strain under study. The isolated S. Infantis strains are pathogenic and antibiotic multi-resistant, and thus, this Salmonella serotype should be under surveillance in the poultry food production chain with the aim of protecting public health.

Identification of antimicrobial resistant bacteria from plant-based food products imported into Canada

The role of plant-based foods in the epidemiology of antimicrobial resistance has been inadequately studied. In this investigation, resistant organisms from vegetables, fruits and spices imported into Canada were identified and characterized. A total of 143 products imported from primarily Asian and African countries were purchased from international markets in Saskatoon, Saskatchewan. Samples were selectively cultured for bacterial species where resistance is known to be emerging. The proportions of samples positive for each organism were as follows: E. coli (n = 13, 9.1%), Salmonella spp. (n = 2, 1.4%), ESBL producing Enterobacter spp. (n = 2, 1.4%) and K. pneumoniae (n = 2, 1.4%), S. aureus (n = 7, 4.9%) and Enterococcus spp. (n = 66, 46.2%). Antimicrobial minimum inhibitory concentrations were determined by broth micro-dilution and agar-dilution. Based on the susceptibility of each organism, isolates were screened for resistance genes (β-lactamases and plasmid mediated quinolones resistance determinants) by PCR. Extended-spectrum β-lactamase producing Enterobacteriaceae and methicillin resistant S. aureus (MRSA) were identified from 6/143 (4.2%) and 2/143 (1.4%) of samples respectively. The qnrB, qnrS and aac(6')-Ib-cr plasmid mediated quinolone resistance determinants were identified in 2/143 (1.4%) of samples tested. None of the Enterobacteriaceae isolates were resistant to meropenem or colistin. Similarly, all Enterococcus isolates remained susceptible to ampicillin, penicillin and vancomycin. Finding multi-drug resistant bacteria which are frequently isolated from human infections is concerning, although the contribution of the global food trade to the dissemination of resistance remains cryptic. These results suggest that imported plant-based foods may be an underappreciated source of clinically relevant resistant organisms. Further study is required to address these gaps in our understanding of the epidemiology of resistance, and the magnitude of the risk posed to human health by these organisms.

Presence and Diversity of Extended-Spectrum Cephalosporin Resistance Among Escherichia coli from Urban Wastewater and Feedlot Cattle in Alberta, Canada

A recent preliminary study from our group found that extended-spectrum cephalosporin-resistance determinants can be detected in the majority of composite fecal samples collected from Alberta feedlot cattle. Most notably, bla_CTX-M genes were detected in 46.5% of samples. Further isolate characterization identified bla_CTX-M-15 and bla_CTX-M-27, which are widespread in bacteria from humans. We hypothesized that Escherichia coli of human and beef cattle origins share the same pool of bla_CTX-M genes. In this study, we aimed to assess and compare the genomic profiles of a larger collection of bla_CTX-M-positive E. coli recovered from fecal composite samples from Canadian beef feedlot cattle and human wastewater through whole-genome sequencing. The variants bla_CTX-M-55, bla_CTX-M-32, bla_CTX-M-27, bla_CTX-M-15, and bla_CTX-M-14 were found in both urban wastewater and cattle fecal isolates. Core genome multilocus sequence typing showed little similarity between the fecal and wastewater isolates. Thus, if the dissemination of genes between urban wastewater and feedlot cattle occurs, it does not appear to be related to the expansion of specific clonal lineages. Further investigations are warranted to assemble and compare plasmids carrying these genes to better understand the modalities and directionality of transfer.

Sharing more than friendship - transmission of NDM-5 ST167 and CTX-M-9 ST69 Escherichia coli between dogs and humans in a family, Finland, 2015

Carbapenemase-producing Enterobacteriaceae (CPE) have rarely been reported in dogs, and never in animals in Finland. However, in April 2015, two meropenem-resistant Escherichia coli were identified from two dogs in one family. Both dogs suffered from chronic otitis externa. Methods: Epidemiological and molecular investigations (pulsed-field gel electrophoresis (PFGE), multilocus sequence typing) were conducted to investigate the source of infection and transmission routes. Results: In both dogs and one family member New Delhi metallo-beta-lactamase (NDM-5)-producing multidrug-resistant ST167 E. coli was found. Whole genome sequencing confirmed that the isolates were identical or only had one or two allelic differences. Additionally, the dogs and humans of the family carried an identical extended-spectrum beta-lactamase (ESBL) CTX-M-group 9 E. coli ST69 strain, indicating interspecies transmission. While the original source remains unclear, human-to-canine transmission is possible. No carbapenems had been administered to the dogs, but exposure to numerous other antimicrobials likely sustained the bacteria and supported its propagation in the canine host. Conclusion: To our knowledge, canine clinical NDM-5 E. coli in Europe, and confirmed CPE transmission between dogs and humans have not been previously reported. The screening of veterinary Enterobacteriaceae isolates for carbapenem resistance is highly recommended.

High prevalence of multidrug resistant Enterobacteriaceae among residents of long term care facilities in Amsterdam, the Netherlands

Introduction

The aim of this study was to determine the rate of asymptomatic carriage and spread of multidrug-resistant micro-organisms (MDRO) and to identify risk factors for extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) carriage in 12 long term care facilities (LTCFs) in Amsterdam, the Netherlands.

Materials and methods

From November 2014 to august 2015, feces and nasal swabs from residents from LTCFs in Amsterdam, the Netherlands were collected and analyzed for presence of multidrug-resistant Gram-negative bacteria (MDRGN), including ESBL-E, carbapenemase-producing Enterobacteriaceae (CPE), colistin-resistant Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Logistic regression analysis was performed to assess associations between variables and ESBL-carriage.

Results

In total, 385 residents from 12 LTCFs (range 15–48 residents per LTCF) were enrolled. The prevalence of carriage of MDRGN was 18.2% (range among LTCFs 0–47%) and the prevalence of ESBL-E alone was 14.5% (range among LTCFs: 0–34%). Of 63 MDRGN positive residents, 50 (79%) were ESBL-E positive of which 43 (86%) produced CTX-M. Among 44 residents with ESBL-E positive fecal samples of whom data on contact precautions were available at the time of sampling, only 9 (20%) were already known as ESBL-E carriers. The prevalence for carriage of MRSA was 0.8% (range per LTCF: 0–7%) and VRE 0%. One CPE colonized resident was found. All fecal samples tested negative for presence of plasmid mediated resistance for colistin (MCR-1). Typing of isolates by Amplified Fragment Length Polymorphism (AFLP) showed five MDRGN clusters, of which one was found in multiple LTCFs and four were found in single LTCFs, suggesting transmission within and between LTCFs. In multivariate analysis only the presence of MDRO in the preceding year remained a risk factor for ESBL-E carriage.

Conclusions

The ESBL-carriage rate of residents in LTCFs is nearly two times higher than in the general population but varies considerably among LTCFs in Amsterdam, whereas carriage of MRSA and VRE is low. The majority (80%) of ESBL-E positive residents had not been detected by routine culture of clinical specimens at time of sampling. Current infection control practices in LTCFs in Amsterdam do not prevent transmission. Both improvement of basic hygiene, and funding for laboratory screening, should allow LTCFs in Amsterdam to develop standards of care to prevent transmission of ESBL-E.

Fecal Colonization of Extended-Spectrum Beta Lactamase-Producing Salmonella spp. in Broilers in Lorestan Province of Iran

Background: Poultry is considered as a major source of human contamination with nontyphoidal Salmonella species. Global concern regarding the emergence and dispersion of extended-spectrum beta-lactamase (ESBLs)-producing isolates in broilers has increased during recent years. Objective: This study was proposed to evaluate the prevalence of Salmonella and the associated ESBLs in broilers in Lorestan province of Iran. Materials and Methods: Five hundred fresh fecal samples of broilers were phenotypically screened for Salmonella. The isolates were confirmed molecularly using an invA-based polymerase chain reaction (PCR). Confirmatory combination disk method was applied for phenotypic detection of ESBLs among the isolates, followed by molecular identification of blaCTX-M, blaTEM, and blaSHV genes in 3 single PCR assays among positive isolates. Chi-square test in SPSS software was used for the assessment of statistical relationships. Results: Of the 95 Salmonella isolates detected using routine bacteriological methods, all were confirmed molecularly. They generated the expected 254-bp amplicon. Moreover, 13 isolates were phenotypically recognized as ESBL determinants, among which 9 and 4 harbored blaCTX-M and blaTEM, respectively. No blaSHV and co-existence of the genes were determined. Conclusion: The threat imposed by dissemination of ESBL-producing non-typhoidal Salmonella spp. isolated from broilers was confirmed in the studied region. Continuous monitoring programs, application of biosecurity measures, and prudent prescription of antibiotics are warranted in order to prevent the introduction or dispersion of the ESBL-producing Salmonella.

Epidemiology and antibiotic resistance trends in clinical isolates of Pseudomonas aeruginosa from Rio de janeiro - Brazil: Importance of mutational mechanisms over the years (1995-2015)

Pseudomonas aeruginosa is a major health concern globally and treating infections caused by MDR-isolates unarguably a humongous challenge that remains an unmet need in modern medicine. To determine patterns and mechanisms of antimicrobial resistance and its spread over the years in Rio de Janeiro, Brazil, 88 P. aeruginosa isolates were selected from 1995 to 2015. Phenotypic and genotypic characterization of antimicrobial resistance was evaluated and isolates were submitted to clonality by PFGE and MLST. PFGE analysis showed a great variability of clonal groups mainly over the past 10 years of this study. STs predominant in the early years (ST804, ST1860, ST487 and ST1602) associated to multidrug resistance (MDR) phenotype were replaced by ST277, ST244, ST1945, ST1791 with extensive drug resistance (XDR) in last years, with significant increase in resistance to carbapenems, fluoroquinolones and aminoglycosides. Colistin resistance was detected in 3.5%. The main mechanisms of antimicrobial resistance were mutational mechanisms (mutations in oprD, mexT and gyrA genes). We found the ESBL genes bla_TEM (n = 2), bla_SHV (n = 3) and bla_CTX (n = 1).The carbapenemases genes was present in ST277 (bla_SPM, n = 3), ST1560 (bla_KPC, n = 3) and ST1944 (bla_KPC, n = 2). The 16S RNA methylase gene (rmtD) was found in five isolates belonged to ST277. In conclusion, molecular epidemiological investigation reveals an increase of antimicrobial resistance in P. aeruginosa over 21 years in Rio de Janeiro with higher population structure and occurrence of high risk clone in the last years. The mutational mechanisms of resistance were present in all XDR isolates.

Non-clonal occurrence of pmrB mutations associated with polymyxin resistance in carbapenem-resistant Klebsiella pneumoniae in Brazil

BACKGROUND

Polymyxins are currently used as a “last-line” treatment for multidrug-resistant Gram-negative infections.

OBJECTIVES

To identify the major mechanisms of resistance to polymyxin and compare the genetic similarity between multi-drug resistant Klebsiella pneumoniae strains recovered from inpatients of public hospitals in the Mid-West of Brazil.

METHODS

97 carbapenems non-susceptible K. pneumoniae were studied. β-lactamases (bla_OXA-48, bla_KPC, bla_NDM, bla_CTX-M, bla_SHV, bla_TEM, bla_IMP, bla_VIM) and mcr-1 to mcr-5 genes were investigated by polymerase chain reaction (PCR). Mutations in chromosomal genes (pmrA, pmrB, phoP, phoQ, and mgrB) were screened by PCR and DNA sequencing. Clonal relatedness was established by using pulsed-field gel electrophoresis and multilocus sequence typing.

FINDINGS

K. pneumoniae isolates harbored bla_KPC (93.3%), bla_SHV (86.6%), bla_TEM (80.0%), bla_CTX-M (60%) genes. Of 15 K. pneumoniae resistant to polymyxin B the authors identified deleterious mutations in pmrB gene, mainly in T157P. None K. pneumoniae presented mcr gene variants. Genetic polymorphism analyses revealed 12 different pulsotypes.

MAIN CONCLUSIONS

Deleterious mutations in pmrB gene is the main chromosomal target for induction of polymyxin resistance in carbapenem-resistant K. pneumoniae in public hospitals in the Mid-West of Brazil.

Distribution of Class 1 and 2 Integrons Among Salmonella Enterica Serovars Isolated from Iranian Patients

Background:

Salmonella entericahas become increasingly resistant to antimicrobial agents, partly as a result of genes carried by integrons.

Objective:

The aim of the present study was to investigate the prevalence of class 1 and 2 integrons and resistance to antimicrobial agents in clinical isolates ofS. enterica.

Methods:

This study included allSalmonellaisolates, recovered from patients with salmonellosis, admitted to Medical Children Hospital, Tehran, Iran during 2015-2016. Bacterial isolates were identified using standard biochemical and agglutination tests. Antimicrobial susceptibility testing was performed according to the Clinical and Laboratory Standards Institute guidelines. The presence of class 1 and 2 integrons was investigated by Polymerase Chain Reaction (PCR) assay, using specific primers.

Results:

A total of 138Salmonellastrains were isolated and included in this study. Integrons were detected in 45 (32%) isolates. Class 1 and 2 integrons were detected in 24 (17.3%) and 21 (15.2%) isolates, respectively. All integron-positive isolates showed multidrug-resistant phenotypes. Resistance to more than three antimicrobial agents was observed in integron-positive isolates.

Conclusions:

Our findings showed that integrons were widely distributed amongS. entericaisolates in Tehran. Class 1 integrons are more prevalent than class 2 integrons inSalmonellaisolates, and there is an association with MDR patterns. Therefore, these integrons are more likely to be involved in the distribution of resistant phenotypes inSalmonellastrains.

Distribution of Clinical NDM-1-Producing Gram-Negative Bacteria in Brazil

New Delhi metallo-β-lactamase (NDM)-producing bacteria have been identified at a worrying rate in Brazil since 2013. Owing to the need to understand the extent of their spread, this study reports the dissemination of bla_NDM in different species of Gram-negative bacilli in different regions and states of Brazil. A total of 81 isolates from nine states were studied, including 11 species. All isolates carried bla_NDM-1 variant and were considered multidrug resistant. Colistin and amikacin were the agents with higher activity compared with the other drugs tested. The findings indicate that the NDM-1 enzyme is already widespread in the country.

Dynamics of cefotaxime resistant Escherichia coli in broilers in the first week of life

Extended-spectrum beta-lactamase producing E. coli (ESBL-E) are wide spread among broilers, with the highest prevalence among individual birds at broiler production farms. Previous research describes low prevalences among individual birds at arrival at the farm (below 30%), and a rapid increase up to 100% within the first week. Our goal was to investigate whether this rapid increase was due to latent contamination of ESBL-E or to contamination at the broiler farm. Two broiler groups, one hatched at a conventional hatchery and the other individually hatched in an ESBL-free environment, were housed individually in an experimental ESBL-free environment. A third group was hatched at a conventional hatchery and kept at a conventional broiler farm. The birds were sampled daily during the first week after hatch and tested for the presence of ESBL-E. In addition ESBL-E presence in eggs that were not incubated was investigated. All birds and eggs came from one ESBL-E positive parent flock. ESBL/AmpC genes, plasmids and E. coli sequence types were determined for a selection of isolates. ESBL-E was never found in the two groups kept in the ESBL-free experimental environment or in the sampled eggs, whereas all broilers sampled at the conventional farm became positive for ESBL-E within three days. One dominant E. coli strain (ST88) carrying bla_CTX-M-1 gene on an IncI1/pST3 plasmid was found in parent and broiler samples. We conclude that the rapid increase in ESBL-E prevalence in the first week of life is not caused by a latent contamination of the majority of birds at arrival, but that this increase must be caused by other factors.

Extended Spectrum Beta-Lactamase (ESBL)-producing bacteria isolated from hospital wastewaters, rivers and aquaculture sources in Nigeria

Untreated wastewater is a risk factor for the spread of antibiotic resistance in the environment. However, little is known about the contribution of untreated wastewater to the burden of antibiotic resistance in the Nigerian environment. In this study, a total of 143 ceftazidime-/cefpodoxime-resistant bacteria isolated from untreated wastewater and untreated wastewater-contaminated surface and groundwater in Nigeria were screened for extended-spectrum β-lactamase (ESBL) genes, integrons and integron gene cassettes by PCR. The genetic environment of bla _CTX-M-15 was mapped by PCR and potentially conjugative plasmids were detected among the isolates by degenerate primer MOB typing (DPMT). ESBL production was confirmed in 114 (79.7%) isolates and ESBL genes (bla _SHV, bla _CTX-M-15 and bla _TEM) were detected in 85 (74.6%) ESBL-producing isolates. bla _CTX-M-15 was associated with ISEcp1 and with orf477 in 12 isolates and with ISEcp1, IS26 and orf477 in six others. To the best of our knowledge, this is the first report of bla _CTX-M-15 in hand-dug wells and borehole serving as sources of drinking water and a first report of the genetic environment of bla _CTX-M-15 in environmental bacteria from Nigeria. The results of this study confirm untreated wastewater as an important medium for the spread of ESBL-producing bacteria within the Nigerian environment. Hence, the widespread practice of discharging untreated wastewater into the aquatic ecosystem in Nigeria is a serious risk to public health.

Fecal carriage of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae in Egyptian patients with community-onset gastrointestinal complaints: a hospital -based cross-sectional study

Objectives

The aim of this study was to determine the prevalence of extended-spectrum β-lactamase (ESBL) and carbapenemase production among Enterobacteriaceae isolated from ambulatory patients with gastrointestinal complaints admitted to El-Ahrar General Hospital, Zagazig, Egypt in the period between January 2013 and May 2013.

Methods

One hundred and thirteen Enterobacteriaceae isolates were recovered from 100 consecutive Egyptian patients with community–onset gastrointestinal complaints. The fecal samples were plated directly on selective EbSA-ESBL Screening Agar and on MacConkey agar. Isolate identification was performed with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Screening for ESBLs and carbapenemases production was done by both the automated VITEK®2 system with AST N198 and by disk diffusion method. Real-time PCR and sequencing were used to characterize the resistance genes. Phylogroups of the E. coli isolates were determined by a triplex PCR-based method.

Results

Of 100 patients screened for fecal colonization with extended-spectrum β-lactamase -producing Enterobacteriaceae (ESBL-E) and carbapenemase- producing Enterobacteriaceae (CPE), 68 were colonized with ESBL-E whereas five patients were positive for CPE. One hundred and thirteen Enterobacterceae isolates were recovered from 100 fecal samples, they belonged to E. coli (n = 72), Klebsiella pneumoniae (n = 23), Enterobacter cloacae(n = 3), Salmonella spp. (n = 1) and other Enterobacterceae isolates (n = 14). The bla_CTX-M gene was detected in 89.04% (65/73) of the ESBL-producing Enterobacteriaceae, whereas bla_SHV and bla_TEM were detected in 30.14% (22/73) and 19.18% (14/73) respectively. Three out of 5 carbapenem-resistant isolates harbored New Delhi metallo-beta-lactamase (NDM) and 2 produced Verona integron-encoded metallo- beta -lactamase (VIM). Twenty-two (47.83%) of the ESBL positive isolates were multidrug resistant (MDR). Phylogenetic analysis showed that, of the 51 ESBL-EC isolates, 17 belonged to group B2, 13 to group D, 11 to group A and 10 to group B1.

Conclusions

Nearly two-thirds of the Enterobacteriaceae isolates recovered from feces of ambulatory patients with community–onset gastrointestinal complaints admitted to El-Ahrar General Hospital, Zagazig, Egypt were ESBL producers and one in every 20 patients included in our study was colonized by carbapenemase-producing Enterobacteriaceae. These high colonization rates are worrying, therefore prudent antimicrobial use should be adopted in Egyptian community settings.

Multiclonal Expansion of Klebsiella pneumoniae Isolates Producing NDM-1 in Rio de Janeiro, Brazil

We characterized NDM-1-producing Klebsiella isolates from Rio de Janeiro, Brazil. PCR was applied for resistance and virulence determinants. The genetic context of bla_NDM was determined by S1 nuclease pulsed-field gel electrophoresis (PFGE) and hybridization. Genotyping was performed by PFGE and multilocus sequence typing (MLST). Most isolates carried multiple resistance genes and remained susceptible to amikacin, fosfomycin-trometamol, polymyxin B, and tigecycline. The spread of NDM-1-producing Klebsiella pneumoniae was not associated with clonal expansion and appears to be associated with Tn3000.

Prevalence and Antibiotic Resistance Profiles of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Healthy Broilers in Shandong Province, China

Food-producing animals carrying extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) have posed a potential threat to human and animal health. However, information regarding ESBL-EC in the intensive broiler breeding areas of Shandong Province, People's Republic of China, is very limited. The goal of our study was to investigate the prevalence and drug resistance characteristics of ESBL-EC in healthy broilers from Shandong Province. A total of 142 ESBL-EC isolates were collected from four prefectures in Shandong Province from October 2014 to February 2015. ESBL-EC isolates were frequently detected (142 of 160 samples, 88.8%) in healthy broilers. Antibiotic susceptibility testing showed that all 142 ESBL-EC isolates were resistant to ampicillin, piperacillin, and cefazolin but were sensitive to imipenem and meropenem. All ESBL-EC isolates carried one or more of the bla genes, in which blaCTX-M, blaTEM-1, and blaSHV-5 genes were identified in 142, 106, and 5 isolates, respectively. The blaCTX-M gene includes blaCTX-M-15 (56), blaCTX-M-65 (42), blaCTX-M-55 (36), blaCTX-M-14 (21), blaCTX-M-79 (1), blaCTX-M-3 (1), blaCTX-M-123 (1), and blaCTX-M-132 (1). In addition, 17 ESBL-EC isolates cocarried the genes of the CTX-M-1 and CTX-M-9 groups. Our findings indicate that healthy broiler flocks in Shandong Province in China are an important reservoir for ESBL-EC, with blaCTX-M and blaTEM-1 being the prevalent resistance genes identified.

Epidemiology, Clinical Presentation, Laboratory Diagnosis, Antimicrobial Resistance, and Antimicrobial Management of Invasive Salmonella Infections

Salmonella enterica infections are common causes of bloodstream infection in low-resource areas, where they may be difficult to distinguish from other febrile illnesses and may be associated with a high case fatality ratio. Microbiologic culture of blood or bone marrow remains the mainstay of laboratory diagnosis. Antimicrobial resistance has emerged in Salmonella enterica, initially to the traditional first-line drugs chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole. Decreased fluoroquinolone susceptibility and then fluoroquinolone resistance have developed in association with chromosomal mutations in the quinolone resistance-determining region of genes encoding DNA gyrase and topoisomerase IV and also by plasmid-mediated resistance mechanisms. Resistance to extended-spectrum cephalosporins has occurred more often in nontyphoidal than in typhoidal Salmonella strains. Azithromycin is effective for the management of uncomplicated typhoid fever and may serve as an alternative oral drug in areas where fluoroquinolone resistance is common. In 2013, CLSI lowered the ciprofloxacin susceptibility breakpoints to account for accumulating clinical, microbiologic, and pharmacokinetic-pharmacodynamic data suggesting that revision was needed for contemporary invasive Salmonella infections. Newly established CLSI guidelines for azithromycin and Salmonella enterica serovar Typhi were published in CLSI document M100 in 2015.

Extended-Spectrum β-Lactamases and/or Carbapenemases-Producing Enterobacteriaceae Isolated from Retail Chicken Meat in Zagazig, Egypt

OBJECTIVES

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.

METHODS

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.

RESULTS

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.

CONCLUSIONS

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.

Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Enterobacteriaceae Isolated from Egyptian Patients with Suspected Blood Stream Infection

Objectives

The aim of the study was to investigate the prevalence of extended-spectrum β-lactamase and carbapenemase production among Enterobacteriaceae isolated from Egyptian patients with suspected blood stream infection.

Methods

Ninety-four Enterobacteriaceae blood culture isolates from Egyptian patients with suspected blood stream infection were collected, one isolate per patient. Identification of bacterial isolates was performed with MALDI-TOF (MS-based Vitek MS system, bioMerieux). Screening for ESBLs and carbapenemases production was done with the Vitek 2 system (bioMérieux). ESBL production was confirmed using the combined disk diffusion method for cefotaxime, ceftazidime, and cefepime, all with and without clavulanic acid (Rosco). Real-time PCR and sequencing were used to characterize the resistance genes. The phylogenetic groups of E. coli were identified by a PCR-based method.

Results

Of the 94 Enterobacteriaceae isolates 46 (48.93%) showed an ESBL phenotype. One Enterobacter spp isolate was ESBL-producer and meropenem-resistant. The genetic analysis showed that CTX-M was present in 89.13% (41/46) of the ESBL-producing Enterobacteriaceae, whereas TEM and SHV were detected in 56.52% (26/46) and 21.74% (10/46) respectively (47.83%) of the ESBL-producing isolates were multidrug resistant (MDR). Eleven out of 30 ESBL-producing E-coli isolates were assigned to phylogroup B2, followed by groups B1 (8 isolates), A (6 isolates) and D (5 isolates).

Conclusions

The high ESBL-E rates (48.93%) found in this study together with the identification of one carbapenem-resistant Enterobacter spp isolate is worrisome. Our results indicate that systems for monitoring and detection of ESBL-producing bacteria in Egyptian hospitals have to be established. Also strict hospital infection control policies with the restriction of the consumption of extended-spectrum cephalosporins are necessary.

Rapid emergence of ESBL producers in E. coli causing urinary and wound infections in Pakistan

Objectives: Production of extended spectrum beta -lactamases (ESBLs) by clinical isolates of pathogenic E. coli is a very serious therapeutic threat. This study was aimed to investigate the prevalence of ESBLs and associated drug resistance in E. coli isolates from urine and pus, and to report the drift from 2005 to 2009-10.

Methodology: Among 173 E. coli isolates, 82 were phenotypically detected as ESBL producers by standard cefotaxime / clavulanic acid and ceftazidime / clavulanic acid disc diffusion tests. Antimicrobial resistance of all ESBL producers was assessed by disc diffusion method. Presence of CTX-M, TEM, SHV and OXA groups was investigated by PCR.

Results: The prevalence of ESBL producing E. coli increased significantly from 33.7% in 2005 to 60.0% in 2009-10 (urine: 31.8% to 62.9%; pus: 41.1% to 55.5%). Resistance to cefotaxime, ceftazidime, ciprofloxacin, gentamicin, nalidixic acid, ticarcillin-clavulanic acid, and trimethoprim-sulfamethoxazole was above 85% in both sets of isolates. Imipenem and Fosfomycin resistance was non-existent in 2005 but ranged from 3-15% in 2009-10. Remarkable increase from 9.5% to 64.7% in urinary tract isolates and from 0 to 55% in pus isolates was observed in colistin sulphate resistance. The dissemination of genes encoding ESBLs was: CTX-M 3.5%; TEM 10.7%; both CTX-M and TEM 3.5% in 2005, and CTX-M 42.5%; TEM 48.1%; both CTX-M and TEM 29.6% in 2009-10.

Conclusions: Our results showed very rapid emergence of multidrug resistant ESBL producing E. coli in Pakistan posing a very serious threat in the treatment of nosocomial and community acquired infections.

The emergence of blaCTX-M-15-carrying Escherichia coli of ST131 and new sequence types in Western China

Background

bla_CTX-M-15, the most widely distributed gene encoding extended-spectrum β-lactamases globally, was not common in China. This study was performed to characterize bla_CTX-M-15-carrying Escherichia coli in western China.

Findings

Out of 144 Escherichia coli isolates from 20 hospitals in western China, 8 were found carrying bla_CTX-M-15. bla_CTX-M-15 was carried by isolates of ST131and 5 new STs (ST3342, ST3513, ST3516, ST3517 and ST3518). The 5 new STs shared 5 identical alleles out of 7 but only had up to 2 alleles identical to ST131. bla_CTX-M-15 was located on plasmids of IncI1 (ST16) or IncFII-related group (four replicon types). The co-transfer of a few antimicrobial resistance genes including qnrA, qnrB, qnrS, qepA, aac (6′)-Ib-cr, aac (3)-II, tetA, bla_TEM and bla_OXA-1 with bla_CTX-M-15 were examined but only bla_TEM-1 was found co-transferring with bla_CTX-M-15.

Conclusions

Five new STs of E. coli and three new types of IncFII-related plasmids carrying bla_CTX-M-15 were identified. This study together with several reports suggested that bla_CTX-M-15 has emerged in China and the interruption of both vertical and horizontal transmission of bla_CTX-M-15 is required to hurdle its further spread.

Genetic mechanisms of antimicrobial resistance identified in Salmonella enterica, Escherichia coli, and Enteroccocus spp. isolated from U.S. food animals

The prevalence of antimicrobial resistance (AR) in bacteria isolated from U.S. food animals has increased over the last several decades as have concerns of AR foodborne zoonotic human infections. Resistance mechanisms identified in U.S. animal isolates of Salmonella enterica included resistance to aminoglycosides (e.g., alleles of aacC, aadA, aadB, ant, aphA, and StrAB), β-lactams (e.g., bla_{CMY−2, TEM−1, PSE−1}), chloramphenicol (e.g., floR, cmlA, cat1, cat2), folate pathway inhibitors (e.g., alleles of sul and dfr), and tetracycline [e.g., alleles of tet(A), (B), (C), (D), (G), and tetR]. In the U.S., multi-drug resistance (MDR) mechanisms in Salmonella animal isolates were associated with integrons, or mobile genetic elements (MGEs) such as IncA/C plasmids which can be transferred among bacteria. It is thought that AR Salmonella originates in food animals and is transmitted through food to humans. However, some AR Salmonella isolated from humans in the U.S. have different AR elements than those isolated from food animals, suggesting a different etiology for some AR human infections. The AR mechanisms identified in isolates from outside the U.S. are also predominantly different. For example the extended spectrum β-lactamases (ESBLs) are found in human and animal isolates globally; however, in the U.S., ESBLs thus far have only been found in human and not food animal isolates. Commensal bacteria in animals including Escherichia coli and Enterococcus spp. may be reservoirs for AR mechanisms. Many of the AR genes and MGEs found in E. coli isolated from U.S. animals are similar to those found in Salmonella. Enterococcus spp. isolated from animals frequently carry MGEs with AR genes, including resistances to aminoglycosides (e.g., alleles of aac, ant, and aph), macrolides [e.g., erm(A), erm(B), and msrC], and tetracyclines [e.g., tet(K), (L), (M), (O), (S)]. Continuing investigations are required to help understand and mitigate the impact of AR bacteria on human and animal health.

Limited diversity in the gene pool allows prediction of third-generation cephalosporin and aminoglycoside resistance in Escherichia coli and Klebsiella pneumoniae

Early appropriate antibiotic treatment reduces mortality in severe sepsis, but current methods to identify antibiotic resistance still generally rely on bacterial culture. Modern diagnostics promise rapid gene detection, but the apparent diversity of relevant resistance genes in Enterobacteriaceae is a problem. Local surveys and analysis of publicly available data sets suggested that the resistance gene pool is dominated by a relatively small subset of genes, with a very high positive predictive value for phenotype. In this study, 152 Escherichia coli and 115 Klebsiella pneumoniae consecutive isolates with a cefotaxime, ceftriaxone and/or ceftazidime minimum inhibitory concentration (MIC) of ≥ 2 μg/mL were collected from seven major hospitals in Sydney (Australia) in 2008-2009. Nearly all of those with a MIC in excess of European Committee on Antimicrobial Susceptibility Testing (EUCAST) resistance breakpoints contained one or more representatives of only seven gene types capable of explaining this phenotype, and this included 96% of those with a MIC ≥ 2 μg/mL to any one of these drugs. Similarly, 97% of associated gentamicin-non-susceptibility (MIC ≥ 8 μg/mL) could be explained by three gene types. In a country like Australia, with a background prevalence of resistance to third-generation cephalosporins of 5-10%, this equates to a negative predictive value of >99.5% for non-susceptibility and is therefore suitable for diagnostic application. This is an important proof-of-principle that should be tested in other geographic locations.

Characterization of bla(SHV) genes on plasmids from Escherichia coli and Salmonella enterica isolates from Canadian food animals (2006-2007)

bla(SHV) genes from Escherichia coli and Salmonella enterica isolates from chicken (n = 19) and pork (n = 1) were identified as bla(SHV-2) (n = 5) or bla(SHV-2a) (n = 15). Eighteen were on plasmids of the incI1 (n = 15), incP (n = 2), and incFIB (n = 1) incompatibility groups. These plasmids were all transferable by conjugation between E. coli and S. enterica.

Diversity of genotypes in CTX-M-producing Klebsiella pneumoniae isolated in different hospitals in Brazil

OBJECTIVE

The present study was undertaken to characterize CTX-M ESBL-producing Klebsiella pneumoniae collected from hospitals in different cities of Brazil.

MATERIAL AND METHODS

Eighty-five K. pneumoniae strains isolated from hospitalized patients in six different hospitals of three cities of Brazil were analyzed. ESBL production was confirmed by the standard double-disk synergy test and the Etest®. The MIC50 and MIC90 for ESBL-producing isolates were determined by the Etest® method. The antimicrobial susceptibilities of bacterial isolates were determined using the agar diffusion method according to the CLSI. Screening for blaTEM, blaSHV, blaCTX-M genes and class 1 integron was performed by PCR amplification. To determine the genomic diversity of CTX-M-producers, isolates were analyzed by macrorestriction profile analysis following PFGE.

RESULTS AND DISCUSSION

Seventy-one K. pneumoniae isolates were ESBL-producing. PCR and sequencing experiments detected 38 CTX-M-producing K. pneumoniae belonged to groups CTX-M 1, CTX-M 2, CTX-M 8 and CTX-M 9. The association of different types ESBL (CTX-M, SHV and TEM) was frequent. All K. pneumoniae isolates carried class 1 integron. PFGE analysis revealed thirty-one clonal types among CTX-M-producing isolates. The data presented herein illustrate the diversity of genotypes of CTX-M producing K. pneumoniae among Brazilians hospitals.

bla(CTX-M)-carrying Escherichia coli of the O25b ST131 clonal group have emerged in China

Six Escherichia coli O25b ST131 isolates, which were mostly hospital-acquired but from various types of samples, were found to carry bla(CTX-M-3a,)bla(CTX-M-14), or bla(CTX-M-65) genes, demonstrating that such isolates have emerged in China. The bla(CTX-M) genes were mostly carried by IncFII-related conjugative plasmids. All isolates were also resistant to ciprofloxacin and gentamicin and had substitutions in GyrA and carried an aac(3)-II gene.

Characterization of the first extended-spectrum beta-lactamase-producing nontyphoidal Salmonella strains isolated in Tehran, Iran

The infections caused by Salmonella remain a significant public health problem throughout the world. beta-Lactams and fluoroquinolones are generally used to treat invasive Salmonella infections, but emergence and spread of antibiotic-resistant strains are being increasingly notified in many countries. In particular, detection of extended-spectrum beta-lactamases (ESBLs) in Salmonella spp. is a newly emerging threat worldwide. This study was carried out to characterize beta-lactamase-producing Salmonella strains identified in Tehran, Iran. Over the 2-year period from 2007 to 2008, 6 of 136 Salmonella isolates recovered from pediatrics patients, including three Salmonella enterica serotypes Enteritidis (S. Enteritidis) and three S. Infantis, showed an ESBL-positive phenotype. Polymerase chain reaction and sequencing were used to identify the genetic determinants responsible for ESBL phenotypes. The Salmonella isolates were also compared by pulsed-field gel electrophoresis. All ESBL-producing strains, but one, carried the bla(CTX-M-15) gene. Moreover, three of four strains that proved to be positive for a bla(TEM) gene were producing a TEM-1 beta-lactamase. Two strains of S. Infantis tested positive for a previously unidentified CTX-M and TEM ESBL, respectively. All ESBL-producing strains carried the insertion sequence ISEcp1 gene. Except for one strain of serotype Infantis, all strains were able to transfer the ESBL determinants by conjugation. Distinct, but closely related, pulsed-field gel electrophoresis patterns were observed among the strains belonging to both serotypes. This study reports for the first time the emergence and characterization of ESBL-producing S. Enteritidis and Infantis strains in Iran.

beta-Lactam resistance in salmonella strains isolated from retail meats in the United States by the National Antimicrobial Resistance Monitoring System between 2002 and 2006

Ampicillin-resistant (Amp(r)) Salmonella enterica isolates (n = 344) representing 32 serotypes isolated from retail meats from 2002 to 2006 were tested for susceptibility to 21 other antimicrobial agents and screened for the presence of five beta-lactamase gene families (bla(CMY), bla(TEM), bla(SHV), bla(OXA), and bla(CTX-M)) and class 1 integrons. Among the Amp(r) isolates, 66.9% were resistant to five or more antimicrobials and 4.9% were resistant to 10 or more antimicrobials. Coresistance to other beta-lactams was noted for amoxicillin-clavulanic acid (55.5%), ceftiofur (50%), cefoxitin (50%), and ceftazidime (24.7%), whereas less than 5% of isolates were resistant to piperacillin-tazobactam (4.9%), cefotaxime (3.5%), ceftriaxone (2%), and aztreonam (1.2%). All isolates were susceptible to cefepime, imipenem, and cefquinome. No Salmonella producing extended-spectrum beta-lactamases was found in this study. Approximately 7% of the isolates displayed a typical multidrug-resistant (MDR)-AmpC phenotype, with resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, tetracycline, plus resistance to amoxicillin-clavulanic acid, cefoxitin, and ceftiofur and with decreased susceptibility to ceftriaxone (MIC > or = 4 microg/ml). Pulsed-field gel electrophoresis results showed that several MDR clones were geographically dispersed in different types of meats throughout the five sampling years. Additionally, 50% of the isolates contained bla(CMY), 47% carried bla(TEM-1), and 2.6% carried both genes. Only 15% of the isolates harbored class I integrons carrying various combinations of aadA, aadB, and dfrA gene cassettes. The bla(CMY), bla(TEM), and class 1 integrons were transferable through conjugation and/or transformation. Our findings indicate that a varied spectrum of coresistance traits is present in Amp(r) Salmonella strains in the meat supply of the United States, with a continued predominance of bla(CMY) and bla(TEM) genes in beta-lactam-resistant isolates.

Molecular characterization and antimicrobial susceptibility of Salmonella isolates from infections in humans in Henan Province, China

We characterized 208 human Salmonella isolates from 2006 to 2007 and 27 human Salmonella enterica serovar Typhimurium isolates from 1987 to 1993 from Henan Province, China, by serotyping, by antimicrobial susceptibility testing, and, for the most common serovars, by pulsed-field gel electrophoresis (PFGE). The most common serovars among the 2006-2007 isolates were S. enterica serovar Typhimurium (27%), S. enterica serovar Enteritidis (17%), S. enterica serovar Derby (10%), S. enterica serovar Indiana (6%), and S. enterica serovar Litchfield (6%). A high percentage of the isolates were multiple-drug resistant, and 54% were resistant to both nalidixic acid and ciprofloxacin. Of these, 42% were resistant to a high level of ciprofloxacin (MIC > 4 microg/ml), whereas for the remaining isolates, the MICs ranged from 0.125 to 2 microg/ml. Five isolates (2%) were ceftiofur resistant and harbored bla(CTX-M14) or bla(CTX-M15). With the possible exception of the quinolones and cephalosporins, the 1987-1993 S. enterica serovar Typhimurium isolates were almost as resistant as the recent isolates. PFGE typing of S. enterica serovar Typhimurium showed that the most common cluster predominated over time. Two other clusters have emerged, and another cluster has disappeared.

Dominance of blaCTX-M within an Australian extended-spectrum beta-lactamase gene pool

bla(CTX-M) genes, particularly bla(CTX-M-15), are the dominant extended-spectrum beta-lactamase (ESBL) genes among clinical isolates of Escherichia coli and Klebsiella pneumoniae in Sydney, Australia, where we also found one example of bla(CTX-M-62), encoding a novel enzyme conferring ceftazidime resistance. ESBL genes were present in diverse community isolates and in a variety of associated conjugative plasmids.

Genetic characterization of clinical and agri-food isolates of multi drug resistant Salmonella enterica serovar Heidelberg from Canada

Background

Salmonella enterica serovar Heidelberg ranks amongst the most prevalent causes of human salmonellosis in Canada and an increase in resistance to extended spectrum cephalosporins (ESC) has been observed by the Canadian Integrated Program for Antimicrobial Resistance Surveillance. This study examined the genetic relationship between S. Heidelberg isolates from livestock, abattoir, retail meat, and clinical human specimens to determine whether there was a link between the emergence of MDR S. Heidelberg in chicken agri-food sources and the simultaneous increase of MDR S. Heidelberg in human clinical samples.

Results

Chromosomal genetic homogeneity was observed by pulsed-field gel electrophoresis (PFGE), DNA sequence-based typing (SBT) and DNA microarray-based comparative genomic hybridization (CGH). Sixty one percent of isolates were indistinguishable by PFGE conducted using XbaI and BlnI restriction enzymes. An additional 15% of isolates had PFGE patterns that were closely related to the main cluster. SBT did not identify DNA polymorphisms and CGH revealed only genetic differences between the reference S. Typhimurium strain and S. Heidelberg isolates. Genetic variation observed by CGH between S. Heidelberg isolates could be attributed to experimental variation. Alternatively, plasmid content was responsible for differences in antimicrobial susceptibility, and restriction fragment length polymorphism (RFLP) analyses followed by replicon typing identified two divergent plasmid types responsible for ESC resistance.

Conclusion

Due to the overall limited genetic diversity among the isolates, it was not possible to identify variable traits that would be suitable for source tracking between human and agri-food isolates of S. Heidelberg in Canada.

Prevalence, antimicrobial resistance, and extended-spectrum beta-lactamases characterization of Salmonella isolates in Apulia, southern Italy (2001-2005)

The prevalence, antimicrobial susceptibility, and production of extended-spectrum beta-lactamases (ESBLs) of Salmonella collected from several hospitals in Apulia (southern Italy) were evaluated. The most common Salmonella isolates were Salmonella enterica serovar Typhimurium (44.6%), S. enterica serovar Enteritidis (33.4 %), S. enterica serovar Infantis (3.2 %), S. enterica serovar Typhi (1.5%), and S. enterica serovar Bovismorbificans (1.5%). The other serovars accounted for less than 1% each. Our data show a high resistance to ampicillin, tetracycline, and chloramphenicol. The isolates were pansensitive (53.5%), resistant to one antimicrobial agent (10.5%), resistant to two antimicrobial agents (22.1%), resistant to three antimicrobial agents (10.8%), and to four antimicrobial agents (2.7%). Resistance to more than four antibiotics was observed in 0.5% of strains. The presence of ESBL was found in only one strain of S. enterica serovar Bovismorbificans. The CTX-M-1 type-producing strain was identified by isoelectric focusing and molecular analysis. Results were consistent with the presence of a pI 8.6 ESBL active on cefotaxime, ceftazidime, cefepime, and aztreonam. Mating experiments showed that the CTX-M-1 determinant was transferable. To the best of our knowledge, this is the first report of CTX-M-1 type ESBL in Salmonella serovar Bovismorbificans.