Phenotypic Antibiotic Resistance Profiles Research Articles

Genomic analysis of Helicobacter pylori in Australia: Antimicrobial resistance, phylogenetic patterns, and virulence factors.

Rates of antimicrobial-resistant Helicobacter pylori infection are rising globally, but little is known about contemporary resistance patterns, virulence factors, and phylogenetic patterns of isolates within Australia. We aimed to characterize antimicrobial resistance and genetic mutations associated with adverse clinical outcomes. Whole genome sequencing, culturing, and antibiotic sensitivity data for refractory H.pylori isolates at Australian centers were collected between 2013 and 2022. Phylogenetic origins, antibiotic resistance mutations, and virulence factors were examined with phenotypic resistance profiles. One hundred thirty-five isolates underwent culture, with 109 of these undergoing whole genome sequencing. Forty-three isolates were isolated from patients in South Australia and 66 from Western Australia. Isolates originated primarily from hpEurope (59.6%), hpEastAsia (25.7%), and hpNEAfrica (6.4%). Antimicrobial resistance to clarithromycin was seen in 85% of isolates, metronidazole in 52%, levofloxacin in 18%, rifampicin in 14%, and amoxicillin in 9%. Most isolates (59%) were multi-drug resistant. Resistance concordance between genetically determined resistance and phenotypic resistance was 92% for clarithromycin and 94% for levofloxacin. Analysis of virulence factors demonstrated cag pathogenicity island (cagPAI) in 67% of isolates and cagA in 61%, correlating with isolate genetic origin. The most virulent s1m1 vacuolating cytotoxin A genotype was present in 26% of isolates. Refractory H.pylori isolates in Australia emanate from multiple global origins. Strong concordance between genetic and phenotypic antibiotic resistance profiles raises the possibility of utilizing genetic profiling in clinical practice. The dynamic landscape of H.pylori in Australia warrants the establishment of a national database to monitor H.pylori resistance and evolving virulence.

Genomic analysis of multidrug-resistant Escherichia coli from Urban Environmental water sources in Accra, Ghana, Provides Insights into public health implications.

Wastewater discharge into the environment in resource-poor countries poses a threat to public health. Studies in this area within these countries are limited, and the use of high-throughput whole-genome sequencing technologies is lacking. Therefore, understanding of environmental impacts is inadequate. The present study investigated the antibiotic resistance profiles and diversity of beta-lactamases in Escherichia coli strains isolated from environmental water sources in Accra, Ghana. Microbiological analyses were conducted on wastewater samples from three hospitals, a sewage and wastewater treatment plant, and water samples from two urban surface water bodies. Confirmed isolates (N = 57) were selected for phenotypic antibiotic resistance profiles. Multi-drug-resistant isolates (n = 25) were genome sequenced using Illumina MiSeq sequencing technology and screened for sequence types, antibiotic resistance, virulence and beta-lactamase genes, and mobile genetic elements. Isolates were frequently resistant to ampicillin (63%), meropenem (47%), azithromycin (46%), and sulfamethoxazole-trimethoprim (42%). Twenty different sequence types (STs) were identified, including clinically relevant ones such as ST167 and ST21. Five isolates were assigned to novel STs: ST14531 (n = 2), ST14536, ST14537, and ST14538. The isolates belonged to phylogroups A (52%), B1 (44%), and B2 (4%) and carried β-lactamase (TEM-1B, TEM-1C, CTX-M-15, and blaDHA-1) and carbapenemase (OXA-1, OXA-181) resistance genes. Dominant plasmid replicons included Col440I (10.2%) and IncFIB (AP001918) (6.8%). Polluted urban environments in Accra are reservoirs for antibiotic-resistant bacteria, posing a substantial public health risk. The findings underscore the need for targeted public health interventions to mitigate the spread of antibiotic-resistant bacteria and protect public health.

Phenotypic Characterization and Plasmid DNA Profiling of Multidrug-Resistant Escherichia coli and Staphylococcus aureus in Wastewater Effluents From Healthcare Environments in Lafia, Nigeria

Background: Multidrug-resistant Escherichia coli and Staphylococcus aureus are frequent culprits of severe healthcare-associated infections and have been identified as significant pollutants in hospital settings. The research into plasmids as potential carriers for transferring new resistance genes among clinical pathogens has been quite constrained. This study was conducted to determine the extent of multidrug resistance and the presence of plasmids in E. coli and S. aureus isolates derived from wastewater effluents at healthcare institutions in Lafia, Nigeria. Methods: A total of 231 effluent samples were collected from different units within the healthcare facilities and bacterial identification performed using standard CLSI identification techniques. Phenotypic multidrug resistance was analyzed using the Kirby-Bauer disc diffusion method while plasmid DNA was extracted by alkaline lysis and separated using 0.8% agarose gel electrophoresis. Results: A total of 167 (72.3%) and 175 (75.6%) samples were positive for E. coli and S. aureus, respectively. Both E. coli and S. aureus exhibited the greatest resistance to amoxicillin, with resistance rates of 79.0% and 66.3%, respectively. Conversely, the lowest resistance was observed for levofloxacin (26.3%) and cotrimoxazole (25.1%) in E. coli and S. aureus, respectively. The study did not find any significant correlation between the phenotypic antibiotic resistance profiles of the isolates and different wastewater discharge points (P>0.05). Out of the total isolates, 77 (46.1%) of E. coli and 51 (29.1%) of S. aureus were resistant to all tested antibiotics. A majority of these isolates exhibited multiple antibiotic resistance index (MARI) values greater than 0.5, with 87.4% of E. coli and 80.6% of S. aureus demonstrating multidrug resistance. Plasmid analysis for E. coli indicated that the largest proportion of the selected isolates (46.7%) carried double plasmids with sizes ranging from 1500 to 6000 base pairs (bp), and 6.7% had no plasmids. In the case of S. aureus, 53.3% of the isolates harbored a single plasmid with a size of 7500 bp, while 46.7% had no plasmids. Conclusion: The wastewater discharged from healthcare facilities in the examined community was found to be significantly contaminated with multidrug-resistant organisms carrying plasmids with resistance genes.

Genotyping and antibiotic susceptibility of Campylobacter species isolated from raw milk samples in Qazvin, Iran

ObjectiveCampylobacter species are major causes of foodborne illnesses, with unpasteurized milk being a significant carrier of these bacteria, posing a public health risk. One of the challenges in managing Campylobacter infections is the emergence and spread of antibiotic resistance. We conducted a study in Qazvin, Iran, testing 84 raw cow’s milk samples to determine the frequency of C. jejuni and C. coli using culture-based and multiplex PCR methods. Additionally, the disk diffusion and RAPD-PCR approaches were utilized to evaluate the phenotypic antibiotic resistance profile and genetic diversity of Campylobacter strains.ResultsThe findings indicated that Campylobacter spp. was present in 19.05% of the samples, with C. coli being the predominant isolate. We tested eight antibiotic agents, and the resistance levels of the isolates were as follows: erythromycin 100%, tetracycline 75%, doxycycline 56.25%, ceftriaxone 43.75%, chloramphenicol 37.5%, amoxicillin-clavulanic acid 25%, nalidixic acid 12.5%, and azithromycin 6.25%. Genetic diversity analysis categorized Campylobacter isolates into 39 clusters, indicating a wide diversity among strains. However, no significant correlation was observed between antibiotic resistance and cluster patterns. These findings underscore the role of raw milk as a reservoir for Campylobacter spp. and highlight the substantial antibiotic resistance and genetic diversity within the species population.

Concordance between Genotypic and Phenotypic Drug-Resistant Profiles of Shigella Isolates from Taiyuan City, Shanxi Province, China, 2005 to 2016.

Antimicrobial resistance in Shigella spp. is a global public health concern. In this study, the AMR phenotypic profiles of 10 kinds of antibiotics were compared with the genotypic profiles using genomic analysis of 218 Shigella isolates from Taiyuan City, Shanxi Province, China, 2005 to 2016. Core genome Multilocus Sequence Typing (cgMLST) based on the EnteroBase Escherichia/Shigella scheme was used to obtain the genetic relatedness of Shigella isolates. Multiple-drug resistance was observed in 96.79% Shigella spp., and the resistance to antimicrobial agents varied between S. flexneri and S. sonnei. The genotypic results correlated well with the phenotypic profiles with concordance rates of 96.42% and 94.50% in S. flexneri and S. sonnei isolates, respectively, from Taiyuan City, Shanxi Province. The sensitivity and specificity of the genotypic antimicrobial susceptibility testing (AST) were 97.56% and 95.34% for S. flexneri, and 95.65% and 93.31% for S. sonnei isolates, respectively. A discrepancy of genotypic and phenotypic AST results existed in some cephalosporin- and azithromycin-resistant Shigella isolates; there were no clear resistance patterns to predict ciprofloxacin resistance. There were major discrepancies between genotypic and phenotypic AST in the genotypically resistant but phenotypically susceptible isolates. The drug-resistance patterns and essential drug-resistance genes to predict the phenotypic drug-resistant profiles were the discrepancies between S. flexneri and S. sonnei isolates. Phylogenetic analysis showed that isolates of the same cluster but with different antibiotic-resistance gene patterns occurred because of the loss or gain of antibiotic-resistance genes located in the plasmids and multidrug-resistance islands. IMPORTANCE Antimicrobial resistance in Shigella spp. has become a global public health concern. In this study, we identified the antimicrobial susceptibility testing (AST) characteristics based on genomic sequences of 218 Shigella isolates and analyzed the correlation between genotypic and phenotypic antibiotic resistance profiles of Shigella spp., especially for fluoroquinolone, macrolides, and third-generation cephalosporins. Our results show that the genotypic results correlated with the phenotypic profiles with concordance rates of 96.42% and 94.50% in S. flexneri and S. sonnei isolates, respectively. The drug-resistance patterns and essential drug-resistance genes to predict the phenotypic drug-resistant profiles of S. flexneri and S. sonnei isolates in Taiyuan city were distinct. The discrepancy between genotypic and phenotypic AST was considerable in the genotypically resistant but phenotypically susceptible isolates. The information on drug resistance and resistance genes in this study can offer more details on the prevalence of drug resistance of Shigella spp.

Antibiotic resistance of isolates of Staphylococcus spp. and Streptococcus spp. causing mastitis on dairy farms in Ukraine

Mastitis is the most common pathology of cows that causes large economic losses to dairy farms. Mastitis is often caused by a group of infectious associated pathogens that can be transmitted among animals. Most often, the pathological process in subclinically and clinically sick animals is caused by coccal gram-positive microflora. A major problem is the mechanisms by which microorganisms acquire resistance to one or more antibacterial agents. Thus, standard treatment regimens used on the farm become ineffective. The publication presents the results of the study of antibiotic resistance of 45 isolates of Staphylococcus spp. and 22 isolates of Streptococcus spp. In this study, the chromogenic media CHROMagarTM Mastitis, CHROMagarTM Orientation and CHROMagarTM MH Orientation were used, which helped to speed up the isolation and identification of cultures. Phenotypic antibiotic resistance profiles were determined using the agar diffusion method. Staphylococcus aureus and coagulase-negative Staphylococcus (CoNS) showed a high level of resistance to beta-lactams of the penicillin class of benzylpenicillin – 60% and 66.7%. Streptococcus disgalactiae and Streptococcus agalactiae showed high resistance to tetracycline – 46.7% and 35.3%. At the same time, Streptococcus agalactiae had a high resistance to clindamycin of 35.3%. Streptococcus disgalactiae to benzylpenicillin – 29.4%, Streptococus uberis to clindamycin – 75%. The lowest resistance was observed to the antibiotic vancomycin in 6.7% of isolated staphylococci and 13.3% of streptococci. MAR index of more than 0.2 was observed in 75% of Streptococus uberis, 60% of CoNS and 52.9% of Streptococcus agalactiae. More than 50% of all studied isolates had multiple resistance to antibiotics most commonly used on Ukrainian farms. Key words: Streptococcus spp., Staphylococcus spp., antibiotic resistance, mastitis, infectious mastitis, gram-positive bacteria.

Distribution pattern of antibiotic resistance genes in Escherichia coli isolated from colibacillosis cases in broiler farms of Egypt.

Multidrug resistance (MDR) of Escherichia coli has become an increasing concern in poultry farming worldwide. However, E. coli can accumulate resistance genes through gene transfer. The most problematic resistance mechanism in E. coli is the acquisition of genes encoding broad-spectrum β-lactamases, known as extended-spectrum β-lactamases, that confer resistance to broad-spectrum cephalosporins. Plasmid-mediated quinolone resistance genes (conferring resistance to quinolones) and mcr-1 genes (conferring resistance to colistin) also contribute to antimicrobial resistance. This study aimed to investigate the prevalence of antimicrobial susceptibility and to detect β-lactamase and colistin resistance genes of E. coli isolated from broiler farms in Egypt. Samples from 938 broiler farms were bacteriologically examined for E. coli isolation. The antimicrobial resistance profile was evaluated using disk diffusion, and several resistance genes were investigated through polymerase chain reaction amplification. Escherichia coli was isolated and identified from 675/938 farms (72%) from the pooled internal organs (liver, heart, lung, spleen, and yolk) of broilers. Escherichia coli isolates from the most recent 3 years (2018-2020) were serotyped into 13 serotypes; the most prevalent serotype was O125 (n = 8). The highest phenotypic antibiotic resistance profiles during this period were against ampicillin, penicillin, tetracycline, and nalidixic acid. Escherichia coli was sensitive to clinically relevant antibiotics. Twenty-eight selected isolates from the most recent 3 years (2018-2020) were found to have MDR, where the prevalence of the antibiotic resistance genes ctx, tem, and shv was 46% and that of mcr-1 was 64%. Integrons were found in 93% of the isolates. The study showed a high prevalence of E. coli infection in broiler farms associated with MDR, which has a high public health significance because of its zoonotic relevance. These results strengthen the application of continuous surveillance programs.

Campylobacter and risk factors associated with dog ownership: a retrospective study in household and in shelter dogs.

Campylobacteriosis has been the most frequently reported zoonotic disease in humans in Europe. The scientific literature has reported that the role of dogs may be relevant. The objectives of this work are to improve the knowledge about Campylobacter spp. carriage, infection and antimicrobial resistance in household and shelter dogs in Italy, and to assess risk factors at the dog/human interface. During the 2015‑2016 period, rectal swabs were collected from 431 household vet‑visiting dogs and 173 dogs housed in shelters. A total of 3 veterinary clinics, located in three Italian regions (Abruzzo, Molise and Tuscany) and 10 shelters, five in Abruzzo and five in Molise, were included in the study. Relevant risk factors for the transmission of Campylobacter spp. from dogs to humans were assessed by means of a questionnaire administered to owners of household dogs. For Campylobacter spp. isolation, selective cultivation methods were used, followed by confirmation and species identification with the PCR method. Phenotypic antibiotic resistance profiles assayed using antimicrobial susceptibility testing were combined. Campylobacter spp. were isolated from 9 household dogs (2.1% CI 1.1% ‑ 3.9%) and from 13 shelter dogs (7.5 % CI 4.5% ‑ 12.4%). In household dogs C. jejuni was the most represented species (0.9%). In shelter dogs, the most common species was C. jejuni (5.2%). Campylobacter spp. isolates were resistant to ciprofloxacin (22.73%), nalidixic acid (22.73%), tetracyclines (27.27%), streptomycin (9.09%) and erythromycin (4.55%). The main C. jejuni Clonal Complex identified in dogs were CC21, CC45, CC206, CC403, CC42 and CC658. The risk of contracting Campylobacteriosis from dogs remains a concrete reality. This risk is increased in the presence of common habits, as shown by the data from the questionnaire. Prevalence control of Campylobacter spp. in household and shelter dogs would be important in order to reduce the transmission to humans.

Data on antibiograms and resistance genes of Enterobacterales isolated from ready-to-eat street food of Ambato, Ecuador.

Foodborne pathogens represent a significant cause of negative impacts on human health and the economy worldwide. Unfortunately, information about epidemiological insights in Latin American countries is scarce. The consumption of ready-to-eat street food in Ecuador is extensive, and information about the presence of foodborne pathogens, their virulence factors, and antimicrobial resistance is negligible. This data includes the occurrence, phenotypic antibiotic resistance profiles, and antibiotic resistance genes of Enterobacterales isolated from ready-to-eat street food in Ambato, central Ecuador during 2020 and 2021. The most common genera detected were Escherichia coli, Klebsiella spp., and Cronobacter spp. Agar disk diffusion assays were performed to determine their phenotypic resistance. The presence of antibiotic resistance genes conferring resistance against colistin, β-Lactams, aminoglycosides, tetracyclines, sulfonamides, fluoroquinolones, and amphenicols was detected via polymerase chain reaction (PCR) amplification.

Antibiotic Resistance and Molecular Characterization of Cronobacter sakazakii Strains Isolated from Powdered Infant Formula Milk.

Background: Cronobacter sakazakii is a new emerging foodborne bacterial pathogen associated with severe lethal diseases such as meningitis, necrotizing enterocolitis, and septicemia in infants and neonates. Powdered infant formula milk (PIFM) has been recognized as one of the main transmission vehicles and contaminated sources of this pathogen. This study aimed to investigate the prevalence rate, genotypic and phenotypic antibiotic resistance profile, and clonal relatedness of C. sakazakii strains isolated from 364 PIFM samples collected from Tehran city, Iran. Methods: Culture-based methods, Kirby–Bauer disk diffusion antibiotic resistance testing, conventional Polymerase Chain Reaction (PCR), and Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR) assays were used in this study to detect and characterize the C. sakazakii isolates. Results: We isolated 25 C. sakazakii strains from PIFM samples (6.86%). The isolates were highly resistant to amoxicillin-clavulanic acid, amoxicillin, ampicillin, cefoxitin, cefepime, erythromycin, ceftriaxone, ciprofloxacin, and chloramphenicol and susceptible to gentamicin, tetracycline, norfloxacin, and azithromycin antibiotics. The blaCTX-M-1 gene was detected in 96% of the isolates. The isolates were categorized into eight distinct clonal types using the ERIC-PCR method, showing a high genetic diversity among the isolates. However, there was a significant correlation between the genotypic and phenotypic antibiotic resistance properties of the isolates. Conclusions: Novel microbial surveillance systems for detecting multi-drug-resistant C. sakazakii are required to control the contamination of this foodborne pathogen in infant foods.

A Preliminary Study on Antimicrobial Susceptibility of Staphylococcus spp. and Enterococcus spp. Grown on Mannitol Salt Agar in European Wild Boar (Sus scrofa) Hunted in Campania Region-Italy.

Simple SummaryDuring the last decade, an increase in the European wild boar (Sus scrofa) population occurred; thus, over the years, wild boars have become an important potential carrier of pathogenic bacteria for both livestock animals and pets, but also for humans. Since antibiotic resistance has become one of the greatest challenges of global public health, the aim of the present study was to define the prevalence and the antibiotic resistance profiles of bacteria grown on the selective medium mannitol salt agar (MSA), isolated from nasal swabs of wild boars hunted in Campania Region (southern Italy). The most prevalent isolated bacteria were represented by the Staphylococcus spp. and Enterococcus spp. strains, which showed worrying antibiotic-resistant profiles. Consequently, constant surveillance of wild boars is strongly recommended, in order to assess their role as reservoirs of antibiotic resistant bacteria and as sentinels of a possible environmental contamination.The importance of wild boar lies in its role as a bioindicator for the control of numerous zoonotic and non-zoonotic diseases, including antibiotic resistance. Mannitol Salt Agar (MSA) is a selective medium used for isolation, enumeration, and differentiation of pathogenic staphylococci. Other genera such as Enterococcus spp. are also salt tolerant and able to grow on MSA. The present study focused on the identification, by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS), of bacteria grown on MSA isolated from the nasal cavities of 50 healthy wild boars hunted in Campania Region (southern Italy) in the year 2019. In addition, the antimicrobial resistance phenotype of the isolated strains was determined by disk diffusion method. Among genus Staphylococcus, coagulase-negative Staphylococcus (CoNS) were the most common isolated species, with Staphylococcus xylosus as the most prevalent species (33.3%). Furthermore, Enterococcus spp. strains were isolated, and Enterococcus faecalis was the species showing the highest frequency of isolation (93.8%). For staphylococci, high levels of resistance to oxacillin (93.3%) were recorded. Differently, they exhibited low frequencies of resistance to tested non-β-lactams antibiotics. Among enterococci, the highest resistances were observed for penicillin (93.7%), followed by ampicillin (75%), and ciprofloxacin (68.7%). Interestingly, 43.7% of the isolated strains were vancomycin-resistant. In conclusion, this study reports the phenotypic antibiotic resistance profiles of Staphylococcus spp. and Enterococcus spp. strains isolated from nasal cavities of wild boars hunted in Campania Region, highlighting that these wild animals are carriers of antibiotic resistant bacteria.

A survey of prevalence and phenotypic and genotypic assessment of antibiotic resistance in Staphylococcus aureus bacteria isolated from ready-to-eat food samples collected from Tehran Province, Iran

BackgroundResistant Staphylococcus aureus (S. aureus) bacteria are considered among the major causes of foodborne diseases. This survey aims to assess genotypic and phenotypic profiles of antibiotic resistance in S. aureus bacteria isolated from ready-to-eat food samples.MethodsAccording to the previously reported prevalence of S. aureus in ready-to-eat food samples, a total of 415 ready-to-eat food samples were collected from Tehran province, Iran. S. aureus bacteria were identified using culture and biochemical tests. Besides, the phenotypic antibiotic resistance profile was determined by disk diffusion. In addition, the genotypic pattern of antibiotic resistance was determined using the PCR.ResultsA total of 64 out of 415 (15.42%) ready-to-eat food samples were contaminated with S. aureus. Grilled mushrooms and salad olivieh harbored the highest contamination rate of (30%), while salami samples harbored the lowest contamination rate of 3.33%. In addition, S. aureus bacteria harbored the highest prevalence of resistance to penicillin (85.93%), tetracycline (85.93%), gentamicin (73.43%), erythromycin (53.12%), trimethoprim-sulfamethoxazole (51.56%), and ciprofloxacin (50%). However, all isolates were resistant to at least four antibiotic agents. Accordingly, the prevalence of tetK (70.31%), blaZ (64.06%), aacA-D (57.81%), gyrA (50%), and ermA (39.06%) was higher than that of other detected antibiotic resistance genes. Besides, AacA-D + blaZ (48.43%), tetK + blaZ (46.87%), aacA-D + tetK (39.06%), aacA-D + gyrA (20.31%), and ermA + blaZ (20.31%) were the most frequently identified combined genotypic patterns of antibiotic resistance.ConclusionReady-to-eat food samples may be sources of resistant S. aureus, which pose a hygienic threat in case of their consumption. However, further investigations are required to identify additional epidemiological features of S. aureus in ready-to-eat foods.

Characterisation of Bacterial Isolates from Infected Post-Operative Patients in a Malaysian Tertiary Heart Care Centre.

Several bacterial species cause post-operative infections, which has been a critical health concern among hospital patients. Our study in this direction is a much-needed exploratory study that was carried out at the National Heart Institute (IJN) of Malaysia to examine the virulence properties of causative bacteria obtained from postoperative patients. The bacterial isolates and data were provided by the IJN. Antibiotic resistance gene patterns, and the ability to form biofilm were investigated for 127 isolates. Klebsiella pneumoniae (36.2%) was the most common isolate collected, which was followed by Pseudomonas aeruginosa (26%), Staphylococcus aureus (23.6%), Streptococcus spp. (8.7%) and Acinetobacter baumannii (5.5%). There were 49 isolates that showed the presence of multidrug resistance genes. The mecA gene was surprisingly found in methicillin-susceptible S. aureus (MSSA), which also carried the ermA gene from those erythromycin-susceptible strains. The phenotypic antibiotic resistance profiles varied greatly between isolates. Findings from the biofilm assay revealed that 44 of the 127 isolates demonstrated the ability to produce biofilms. Our findings provide insights into the possibility of some of these bacteria surviving under antibiotic stress, and some antibiotic resistance genes being silenced.

Prevalence of ESBL, AmpC and Carbapenemase-Producing Enterobacterales Isolated from Raw Vegetables Retailed in Romania.

(1) Background: As β-lactamase-producing Enterobacterales are no longer exclusively associated with the health care system, investigating the potential risk they pose to the integrity of the environment and food safety has become of utmost importance. This study aimed to determine the prevalence of extended-spectrum β-lactamase (ESBL), AmpC, and carbapenemase-producing Enterobacterales isolates from retailed raw vegetables and to determine if household washing is an effective method of lowering bacterial load; (2) Methods: Seasonal vegetables (n = 165) were acquired from supermarkets (n = 2) and farmer markets (n = 2) in Romania. Following sample processing and isolation, identification of Enterobacterales was performed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF). Polymerase chain reaction (PCR) multiplex was used to ascertain the presence of the main ESBL, AmpC, and Carbapenemase genes. Phenotypic antibiotic resistance profiles of isolates were determined by extended antibiograms. Enterobacteriaceae colony-forming units (CFU) counts were compared between vegetable types; (3) Results: Beta-lactamase producing bacteria were observed on 7.9% of vegetables, with 5.5% displaying ESBL/AmpC phenotype and 2.4% identified as Carbapenemase producers. The most frequently detected β-lactamase genes were blaSHV (n = 4), followed by blaCTX-M and blaTEM (each with n = 3). Phenotypic antibiotic resistance analysis showed that 46% of isolates were multiple drug resistant, with aminoglycosides (38.5%) the most prevalent non-β-lactam resistance, followed by first-generation quinolones (38.5%). (4) Conclusions: The present study has described for the first time the presence of β-lactamase producing Enterobacterales in fresh produce retailed in Romania.

Analysis of phenotypic antibiotic resistance profile of Staphylococcus aureus from community settings of a university campus

Background: The multivariate analysis distinguishes components or factors and establishes associations among antibiotics based on their different levels of correlation. Objectives: A dendrogram analysis utilizing the clustering algorithm and comparative multivariate analysis on the Minimum Inhibitory Concentration (MICs) of eleven antibiotics, including the vancomycin, was performed. Methods: A sum of 37 phenotypic resistance profile of S. aureus [10 methicillin-resistant S. aureus (MRSA)], isolated from various community settings of university campuses including Guru Angad Dev Veterinary and Animal Sciences University (GADVASU) and Punjab Agriculture University (PAU), were preselected.

Poultry and beef meat as potential seedbeds for antimicrobial resistant enterotoxigenic Bacillus species: a materializing epidemiological and potential severe health hazard

Although Bacillus cereus is of particular concern in food safety and public health, the role of other Bacillus species was overlooked. Therefore, we investigated the presence of eight enterotoxigenic genes, a hemolytic gene and phenotypic antibiotic resistance profiles of Bacillus species in retail meat samples. From 255 samples, 124 Bacillus isolates were recovered, 27 belonged to B. cereus and 97 were non-B. cereus species. Interestingly, the non-B. cereus isolates carried the virulence genes and exhibited phenotypic virulence characteristics as the B. cereus. However, correlation matrix analysis revealed the B. cereus group positively correlates with the presence of the genes hblA, hblC, and plc, and the detection of hemolysis (p < 0.05), while the other Bacillus sp. groups are negatively correlated. Tests for antimicrobial resistance against ten antibiotics revealed extensive drug and multi-drug resistant isolates. Statistical analyses didn’t support a correlation of antibiotic resistance to tested virulence factors suggesting independence of these phenotypic markers and virulence genes. Of special interest was the isolation of Paenibacillus alvei and Geobacillus stearothermophilus from the imported meat samples being the first recorded. The isolation of non-B. cereus species carrying enterotoxigenic genes in meat within Egypt, suggests their impact on food safety and public health and should therefore not be minimised, posing an area that requires further research.

Occurrence of Salmonella enterica and Escherichia coli in raw chicken and beef meat in northern Egypt and dissemination of their antibiotic resistance markers

BackgroundThe global incidence of foodborne infections and antibiotic resistance is recently increased and considered of public health concern. Currently, scarcely information is available on foodborne infections and ESBL associated with poultry and beef meat in Egypt.MethodsIn total, 180 chicken and beef meat samples as well as internal organs were collected from different districts in northern Egypt. The samples were investigated for the prevalence and antibiotic resistance of Salmonella enterica serovars and Escherichia coli. All isolates were investigated for harbouring class 1 and class 2 integrons.ResultsOut of 180 investigated samples 15 S. enterica (8.3%) and 21 E. coli (11.7%) were isolated and identified. S. enterica isolates were typed as 9 S. Typhimurium (60.0%), 3 S. Paratyphi A (20.0%), 2 S. Enteritidis (13.3%) and 1 S. Kentucky (6.7%). Twenty-one E. coli isolates were serotyped into O1, O18, O20, O78, O103, O119, O126, O145, O146 and O158. The phenotypic antibiotic resistance profiles of S. enterica serovars to ampicillin, cefotaxime, cefpodoxime, trimethoprim/sulphamethoxazole and tetracycline were 86.7, 80.0, 60.0, 53.3 and 40.0%, respectively. Isolated E. coli were resistant to tetracycline (80.9%), ampicillin (71.4%), streptomycin, trimethoprim/sulphamethoxazole (61.9% for each) and cefotaxime (33.3%). The dissemination of genes coding for ESBL and AmpC β-lactamase in S. enterica isolates included blaCTX-M (73.3%), blaTEM (73.3%) and blaCMY (13.3%). In E. coli isolates blaTEM, blaCTX-M and blaOXA were identified in 52.4, 42.9 and 14.3%, respectively. The plasmid-mediated quinolone resistance genes identified in S. enterica were qnrA (33.3%), qnrB (20.0%) and qnrS (6.7%) while qnrA and qnrB were detected in 33.3% of E. coli isolates. Class 1 integron was detected in 13.3% of S. enterica and in 14.3% of E. coli isolates. Class 2 integron as well as the colistin resistance gene mcr-1 was not found in any of E. coli or S. enterica isolates.ConclusionsThis study showed high prevalence of S. enterica and E. coli as foodborne pathogens in raw chicken and beef meat in Nile Delta, Egypt. The emergence of antimicrobial resistance in S. enterica and E. coli isolates is of public health concern in Egypt. Molecular biological investigation elucidated the presence of genes associated with antibiotic resistance as well as class 1 integron in S. enterica and E. coli.

Population Diversity of Campylobacter jejuni in Poultry and Its Dynamic of Contamination in Chicken Meat.

This study aimed to analyse the diversity of the Campylobacter jejuni population in broilers and to evaluate the major source of contamination in poultry meat. Eight rearing cycles over one year provided samples from three different broiler farms processed at the same slaughterhouse. A total of 707 C. jejuni were isolated from cloacal swabs before slaughter and from the breast skin of carcasses after slaughter and after chilling. All suspected Campylobacter colonies were identified with PCR assays and C. jejuni was genotyped by sequence analysis of the flaA short variable region (SVR) and by pulsed-field gel electrophoresis (PFGE) using SmaI enzyme. Phenotypic antibiotic resistance profiles were also assayed using minimal inhibitory concentration (MIC). The flocks carried many major C. jejuni clones possibly carrying over the rearing cycles, but cross contamination between farms may happen. Many isolates were resistant to fluoroquinolones, raising an issue of high public concern. Specific Campylobacter populations could be harboured within each poultry farm, with the ability to contaminate chickens during each new cycle. Thus, although biosecurity measures are applied, with a persistent source of contamination, they cannot be efficient. The role of the environment needs further investigation to better address strategies to control Campylobacter.

Salmonella enterica serotype Kentucky associated with human infections in Switzerland: Genotype and resistance trends 2004–2009

Salmonella serotype Kentucky emerged since 2002 and now ranks among the top ten serovars isolated from humans in Europe, and 8th to 10th in Switzerland. A total of 106 strains isolated from different patients from 2004 through 2009 in Switzerland were further characterized by (i) assessing phenotypic antibiotic resistance profiles using the disk diffusion method and (ii) by genotyping using pulsed-field gel electrophoresis (PFGE) after macrorestriction with XbaI in order to evaluate strain relationships and trends.In Switzerland, there is evidence for an outbreak in 2006 as the annual incidence almost doubled. A total of 30 strains (28%) were resistant or showed intermediate resistance to one to three antimicrobials and 48 strains (45%) displayed resistance to more than three antibiotics. We found a high prevalence (67%) of nalidixic acid resistance, and 58% were resistant to ciprofloxacin. One strain was a producer of extended-spectrum β-lactamase (ESBL). PFGE discriminated four clusters (similarity coefficient cut off at 80%).The resistance situation among the strains isolated from 2004 to 2009 in Switzerland is discussed and shown to coincide with findings in other European countries. Based on genetic subtyping, a so far undetected outbreak is likely to have occurred in Switzerland in 2006. Finally, our data identified travelling to Northern Africa as a risk factor for S. Kentucky infections.

Salmonella entericaserotype Virchow associated with human infections in Switzerland: 2004-2009

BackgroundSalmonellosis is one of the most important foodborne diseases and a major threat to public health. Salmonella serotype Virchow ranks among the top five serovars in Europe.MethodA total of 153 strains isolated from different patients from 2004 through 2009 in Switzerland were further characterized by (i) assessing phenotypic antibiotic resistance profiles using the disk diffusion method and (ii) by genotyping using pulsed-field gel electrophoresis (PFGE) after macrorestriction with XbaI in order to evaluate strain relationship.ResultsThe relative frequency of S. Virchow among other Salmonella serovars varied between 4th to 8th rank. The annual incidence ranged from 0.45/100'000 in 2004 to 0.40/100'000 in 2009. A total of 48 strains (32%) were resistant to one to 3 antimicrobials, 54 strains (36%) displayed resistance patterns to more than three antibiotics. No trend was identifiable over the years 2004 to 2009. We found a high prevalence (62%) of nalidixic acid resistant strains, suggesting an equally high rate of decreased fluoroqionolone susceptibility, whereas intermediate resistance to ciprofloxacin was negligible. Two strains were extended spectrum β-lactamase (ESBL) producers. Analysis of PFGE patterns uncovered a predominant cluster (similarity coefficient above 80%) consisting of 104 of the 153 strains.ConclusionThe worldwide increase of antibiotic resistances in Salmonella is an emerging public health problem. For Switzerland, no clear trend is identifiable over the years 2004 to 2009 for S. Virchow. Antimicrobial susceptibility and resistance profiles varied considerably within this period. Nevertheless, the situation in Switzerland coincided with findings in other European countries. Genotyping results of this strain collection revealed no evidence for an undetected outbreak within this time period.