Antimicrobial Resistance Typing Research Articles

Antimicrobial Resistance and Genomic Characterization of Salmonella Isolated from Pigeons in China

Salmonellosis is one of the important bacterial infectious diseases affecting the health of pigeons. Heretofore, the epidemiological characteristics of Salmonella in pigeon populations in China remain largely unclear. The present study investigated the antimicrobial resistance and genomic characteristics of Salmonella isolates in pigeons in different regions of China from 2022 to 2023. Thirty-two Salmonella isolates were collected and subjected to 24 different antimicrobial agents, representing nine categories. The results showed that these isolates were highly resistant to cefazolin (100%), gentamicin (100%), tobramycin (100%), and amikacin (100%). Three or more types of antimicrobial resistance were present in 90.62% of the isolates, indicating multidrug resistance. Furthermore, using whole genome sequencing technology, we analyzed the profiles of serotypes, multilocus sequence typing, virulence genes, antimicrobial resistance genes, and plasmid replicons and constructed phylogenetic genomics to determine the epidemiological correlation among these isolates. All strains belonged to Salmonella Typhimurium var. Copenhagen and exhibited five antimicrobial resistance genes and more than 150 Salmonella virulence genes. Moreover, each isolate contained both the IncFIB(S) and IncFII(S) plasmids. In addition, phylogenetic analysis showed that all isolates were very close to each other, and isolates from the same region clustered in the same branch. Overall, our findings provide the first evidence for the epidemiological characteristics of Salmonella in pigeons of China, highlighting the importance of preventing salmonellosis in pigeons.

Microbiological sampling and analyses in the food business operators’ HACCP-based self-control programmes

A questionnaire was developed within the OH-HARMONY-CAP project providing an overview of current procedures for microbiological sampling and analyses in food business operators’ HACCP-based self-control programmes in EU/EEA countries. It focused on six bacterial species: Salmonella spp., Listeria monocytogenes, Campylobacter spp., Shiga toxin-producing Escherichia coli, Shigella spp. and Yersinia spp.; and five parasites: Trichinella spp., Cryptosporidium spp., Echinococcus granulosus (Sensu lato), Echinococcus multilocularis and Toxoplasma gondii. Participating EU/EEA countries distributed the questionnaire to food business operators’ laboratories within their countries and responses were received from nine countries. Feedback from 35 laboratories among 554 were considered for data analysis. Results showed that dairy products were analysed most frequently and the majority of laboratories analysed both ready-to-eat and non-ready-to-eat products. Laboratories analysing Salmonella spp. and Listeria monocytogenes processed the majority of samples. Accreditation for ISO-standards or an alternative method was in place in a considerable proportion of laboratories, but did not cover all pathogens investigated. Sending isolates for further confirmation to external laboratories was not common. In contrast, storing isolates was more frequently established. Around 60% of laboratories used more than one typing or characterisation method, predominantly MALDI-TOF, antimicrobial resistance typing and PCR, while 40% did not use any of these methods. Variability was observed as regards use of Whole Genome Sequencing; and participation in External Quality Assessment programmes. The study gathered insight into current practices of microbiological sampling and analyses performed in food business operators’ HACCP-based self-control programmes, and showed that further efforts are needed for harmonisation of analytical protocols and characterisation of foodborne pathogens.

The Significance of Epidemic Plasmids in the Success of Multidrug-Resistant Drug Pandemic Extraintestinal Pathogenic Escherichia coli.

Epidemic IncF plasmids have been pivotal in the selective advantage of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC). These plasmids have offered several advantages to their hosts that allowed them to coevolve with the bacterial host genomes and played an integral role in the success of ExPEC. IncF plasmids are large, mosaic, and often contain various types of antimicrobial resistance (AMR) and virulence associated factor (VAF) genes. The presence of AMR, VAF genes, several addition/restriction systems combined with truncated transfer regions, led to the fixation of IncF plasmids in certain ExPEC MDR clones, such as ST131 and ST410. IncF plasmids entered the ST131 ancestral lineage in the mid 1900s and different ST131 clade/CTX-M plasmid combinations coevolved over time. The IncF_CTX-M-15/ST131-C2 subclade combination emerged during the early 2000s, spread rapidly across the globe, and is one of the greatest clone/plasmid successes of the millennium. The ST410-B3 subclade containing blaCTX-M-15 incorporated the NDM-5 carbapenemase gene into existing IncF platforms, providing an additional positive selective advantage that included the carbapenems. A "plasmid-replacement" clade scenario occurred in the histories of ST131 and ST410 as different subclades gained different AMR genes on different IncF platforms. The use of antimicrobial agents will generate selection pressures that enhance the risks for the continuous emergence of MDR ExPEC clone/IncF plasmid combinations. The reasons for clade/IncF replacements and associations between certain clades and specific IncF plasmid types are unknown. Such information will aid in designing management and prevention strategies to combat AMR.

Treatment of severe infections caused by ESBL or carbapenemases-producing Enterobacteriaceae

Enterobacteriaceae are the most frequent pathogens in the Intensive Care Unit. Due to their safety and activity, β-Lactams (BL) and carbapenems represented the most common strategy adopted against these germs. The increasing exposure to these molecules led to the development of several types of antimicrobial resistance as the expression of extended-spectrum β-lactamases (ESBLs) and carbapenemases. Great molecular variability exists among these enzymes, with significant clinical impact.To limit morbidity and mortality, old antibiotics were tested and represent viable alternatives for specific types of infections, or once the spectrum of susceptibility of each germ has been determined. Alongside, new molecules have been specifically designed but enzyme molecular variability prevents the existence of one single antibiotic which fits for all.Therefore, a quicker identification of the molecular identity of each germ, together with the knowledge of the activity spectrum of each antibiotic is crucial to tailor the therapy and make it effective.

Metagenomics: An Approach for Unraveling the Community Structure and Functional Potential of Activated Sludge of a Common Effluent Treatment Plant

The common effluent treatment plant (CETP) located at Baddi treats the industrial effluent from various industries, leading to the pooling of a diverse range of substrates and metabolites. The nutrient loading and its availability decide the balance of the microbial community and its diversity. The samples thus collected from the activated sludge (BS14) of CETP and Sirsa river (SR1) from the vicinity of CETP effluent discharge were processed for the whole metagenome analysis to reveal the microbial community and its functional potential. The taxonomic classification of the BS14 sample showed the dominance of the bacterial community with 96% of abundance, whereas the SR1 was populated by eukaryotes representing 50.4% of the community of SR1. The bacterial community of SR1 was constituted of 47.2%. The functional analysis of BS14 and SR1 with GhostKOALA against the KEGG database assigned 43.7% and 27.8% of the open reading frames (ORFs) with functions. It revealed the xenobiotic degradation modules with complete pathways along with resistance against the beta-lactams. The analysis with the comprehensive antibiotic resistance database (CARD) revealed 33 and 32 unique types of antimicrobial resistance in BS14 and SR1, respectively. Both the samples were dominated by the beta-lactam resistance genes. The carbohydrate-active enzyme (CAZy) database assigned a total of 6,611 and 2,941 active enzymes to BS14 and SR1, respectively. In contrast, the glycosyl hydrolases (GH) and glycosyltransferases (GT) class of enzymes were found to be abundant in both the samples as compared with polysaccharide lyases (PL), auxiliary activities (AA), carbohydrate esterases (CE), and carbohydrate-binding module (CBM).

MICROBIOLOGICAL ISOLATES AND IT’S RESISTOTYPE FROM CLINIC OF VASCULAR SURGERY FOR THE FIRST QUATER OF 2022

One of the most common complications of surgical exposures is the surgical site infection (SSI). Although it varies between different surgical profiles, it can reach up to one third of all complications. In vascular surgery patients ischemic ulcers are very common, as well as factors, compromising the immune system such as diabetes, chronic kidney disease etc. One of the main surgical exposures in vascular surgery is inguinal, providing access to the femoral artery and its bifurcation. Although it allows a wide range of reconstructions, implanting different types of prosthetic materials, stents and providing anastomosis site, it contains lymph nodes, which can contaminate the reconstruction and cause SSI with severe consequences. Patients, prone to SSI due to concomitant diseases, are threatened by sepsis, limb loss and even death, which makes prevention of those type of complications essential. Aim: To investigate etiological spectrum of microbiological isolates and their resistance against most common antimicrobials among vascular surgery patients. Materials and methods: The study is retrospective, conducted in the period 01 January 2022 – 31 March 2022. All of the samples were obtained from patients of Clinic of Vascular Surgery. After isolation of pure culture from the samples, the strains were identified by MALDI TOF MS and Vitec – 2 Compact. Antibiotic resistance was determined with Bauer-Kirby disk diffusion method. Results: From all 419 of the patients, hospitalized in the Clinic of Vascular surgery for this period, 28 isolates from 26 (6,21%) patients were obtained, of which Gram-negative were 19 (67,86%) and Gram-positive - 9 (32,14%). From Gram-negative - enterobacteria – 14 (73,68%), and non-fermenting gram-negative bacteria (NFGNB) were 5 (26,32%). Only 3 (21,43%) from all enterobacteria were extended spectrum beta-lactamases producing strains (ESBLs). No strains, resistant to carbapenems (RCP) were isolated. Five (55,55%) of the Gram-positive isolates were Staphylococcus aureus, 4 (80%) of which were methicillin resistant Staphylococcus aureus (MRSA). Two of the Gram-positive species isolated were Enterococcus faecalis, of which 1 with a high-level aminoglycoside resistance (HLAR). No Vancomycin resistant enterococci (VRE) were discovered. There were no colistin-resistant Acinetobacter baumannii and Pseudomonas aeruginosa strains. Conclusion: From all 28 isolates 8 (28,57%) were with acquired types of antimicrobial resistance. With almost one third of the isolates that are problematic in terms of antibiotic susceptibility, treatment of those patients can be challenging. Prevention of in hospital contamination with polyresistant strains, associated with medical care it is crucial for reducing the number of severe complications, decreasing of hospital stay and cost for treatment.

Effects of management strategies during early lactation and weaning on etiological agents of ovine subclinical mastitis and antimicrobial susceptibility of milk-derived bacterial isolates.

Subclinical mastitis is a common intramammary disease in sheep production systems. Expenses associated with compromised animal performance, therapeutic interventions, and decreased ewe longevity make efforts to minimize its prevalence worthwhile. The objectives of this study were to 1) quantify the prevalence of subclinical mastitis throughout lactation, 2) evaluate the impact of bedding treatments on subclinical mastitis during early lactation, 3) evaluate the efficacy of prophylaxis and feed restriction during weaning on subclinical mastitis cure rates, and 4) identify levels and types of antimicrobial resistance in milk-derived bacteria. Ewe milk samples were collected at days 1, 2, and 28 post-partum, weaning, and 3-d post-weaning for bacterial identification via culture-based methods. Staphylococcus spp. and Streptococcus spp. isolates were subjected to in vitro antimicrobial susceptibility testing. The overall prevalence of subclinical mastitis defined by culture growth ranged between 22% and 66% and differences were observed between post-weaning and days 1 and 28 milk samples. Commonly isolated bacteria include coagulase-negative staphylococci (CoNS; 59%), Bacillus spp. (35%), Mannheimia haemolytica (10%), Staphylococcus aureus (8%), Streptococcus spp. (5%), and Corynebacterium spp. (5%). Early milk samples (days 1 and 2) were compared between jug bedding treatment: jugs were recently vacated, cleaned, and dusted with barn lime before adding fresh straw (CLEAN) or jugs were previously vacated and fresh straw was added atop soiled bedding (SOILED). Jug bedding treatment did not affect the prevalence of subclinical mastitis, though CoNS had greater sulfadimethoxine resistance in SOILED isolates than CLEAN isolates (P = 0.03). Three different weaning treatments were used: ewes were injected with penicillin at weaning (PENN), ewes had restricted feed access 48 h prior to and 72 h post-weaning (FAST), or a combination of these treatments (COMBO). Weaning treatment did not affect the prevalence of subclinical mastitis or cure rate from weaning to 3-d post-weaning, though all PENN and no FAST milk S. aureus isolates were resistant against tetracycline (P = 0.08). Subclinical mastitis prevalence tended to decrease from weaning to post-weaning (P = 0.08). These data show that subclinical mastitis is common throughout lactation and the levels of antimicrobial resistance of bacteria isolated from ewe milk are generally low against commonly used antimicrobials.

Research note: The resistome of commensal Escherichia coli isolated from broiler carcasses “produced without the use of antibiotics”a

Several strategies have been in place in food animal production to reduce the unnecessary use of antimicrobial agents. Beyond the monitoring of their use, the evaluation of the effect of these strategies on the occurrence and types of antimicrobial resistance (AMR) associated genes is crucial to untangle the potential emergence and spread of AMR to humans through the food chain. In the present study, the occurrence of these genes was evaluated in commensal Escherichia coli isolated from broiler carcasses “produced without the use of antibiotics” in 3 antibiotic-free (AB-free) farms in Italy in 2019. Sequenced data were analyzed along with publicly available genomes of E. coli collected in Italy from the broiler food chain from previous years (2017–2018). The genetic relationships among all 93 genomes were assessed on de novo assemblies by in silico MLST and SNP calling. Moreover, the resistomes of all genomes were investigated. According to SNP calling, genomes were gathered in three clades. Clade A encompassed, among others, ST117, ST8070, and ST1011 genomes. ST10 belonged to clade B, whereas Clade C included ST58, ST297, ST1101, and ST23 among others. Regarding the occurrence of AMR genes, a statistically significant lower occurrence of these genes in the genomes of this study in comparison to the public genomes was observed considering the whole group of genes as well as genes specifically conferring resistance to aminoglycosides, β-lactams, phenicols, trimethoprim, and lincosamides. Moreover, significant reductions were observed by comparing the whole group of AMR associated mutations, as well as those specifically for fluoroquinolones and fosfomycin resistance. Although the identification of 3° generation cephalosporin resistance associated genes in AB-free E. coli is a concern, this study provides a first indication of the impact of a more prudent use of antimicrobial agents on the occurrence of AMR genes in Italian broiler production chain. More studies are needed in next years on a higher number of genomes to confirm this preliminary observation.

Community delivered outpatient parenteral antimicrobial therapy in Qatar

Background: For some time, paramedics and nurses of the National Ambulance Service in Qatar provided outpatient parenteral antimicrobial therapy (OPAT) to patients with the support of Family Physicians. Like in many other countries of the Middle East, there is a high prevalence of antimicrobial resistance which makes treating infectious conditions challenging. Methods: This is a retrospective cohort study of patients referred to the Ambulance Service – Mobile Healthcare Service from a public hospital acute facility for OPAT over 6 months in 2015. The study's primary aim is to determine whether the OPAT service had comparable outcomes to international reports with respect to unplanned hospital visits for acute care within 30 days of OPAT referral. A secondary aim of this work is to determine the effect of body fluid culture results on that outcome by comparing subgroups within the OPAT population, and the documentation of prevalence and types of antimicrobial resistance. Results: Between the 1st of March and the 30th of August 2015, 232 OPAT referrals were received. The most common referral diagnoses are reported in Table 1. Within 30 days of OPAT referral, 24.1% - 30.7% of patients required an unplanned hospital visit. This is at the high end of the range reported internationally for OPAT services.1,2 Patients with resistant bacterial infections isolated from body fluid cultures experienced the worst outcomes. The prevalence of significant drug resistance among OPAT referrals was 28.0%, mostly extended-spectrum β-lactamase (ESBL) production. Conclusion: OPAT can be provided in the community.3 The rate of return to hospital for acute care within 30 days of OPAT referral was relatively high, however much of this can be accounted for by patients with resistant infections. They had worse outcomes than patients with non-resistant infections or those treated on an empiric basis. The prevalence of antimicrobial resistance was comparable with other recent Middle Eastern reports.

Hospital liquid waste contaminated with multidrug-resistant bacteria raises a public health hazard alert in Brazil.

The spread of multidrug-resistant bacteria (MDR) is a global concern because it poses a serious threat to public health. The inadequate handling of Health Services Waste (HSW) and, therefore, the incorrect disposal of infected liquids can cause contamination of the environment, the emergence of diseases caused by MDR bacteria, and the loss of the population's quality of life. The present study aimed to survey the bacteria and their antimicrobial resistance profiles, present in the liquid residues from infected surgeries performed in fiveyears, often discharged into the sewage network of a large tertiary hospital located in the city of Uberlândia, which is considered one of the main economic and demographic centers of Brazil. A systematic and retrospective survey of the medical records of patients who underwent infected surgeries from January 2015 to December 2019 was carried out at the referred hospital. The bacterial species were previously identified and characterized for the antimicrobial susceptibility profile by the VITEK 2 automated system (bioMérieux, Brazil). In the evaluated period, 1658 infected surgeries were performed and the results showed 661 bacterial strains distributed in 48 different species, being Staphylococcus aureus the most prevalent species. The vast majority (85.6%) showed some type of antimicrobial resistance among these strains, with more than half (54.6%) being MDR. The results of this work raise an alert and concern for the risks to the environment and public health by dumping these infected liquid wastes directly into the sewage system without proper prior decontamination.

Determination and molecular analysis of antibiotic resistance in Gram-negative enteric bacteria isolated from Pelophylax sp. in the Eastern Black Sea Region.

The aim of this study was to evaluate the prevalence and types of antimicrobial resistance among Gram-negative enteric bacteria isolated from Pelophylax sp. Fifty-four frogs were collected from six provinces in the Eastern Black Sea Region of Turkey. In the cloacal swab cultures, bacteria from 160 different colonies were identified by biochemical tests, automated systems, and matrix-assisted laser desorption ionisation-time of flight mass spectrometry. The antimicrobial susceptibility tests were performed by the disk diffusion method. The observed drug resistance rate was the highest to ampicillin and cefazolin, while the lowest against ciprofloxacin and tetracycline. In the molecular assays, bla TEM (8 Citrobacter spp.), bla SHV (2 Escherichia coli, 1 Hafnia alvei, and a Serratia liquefaciens), tetA genes (E. coli and Klebsiella spp.) and a class 1 integron without any gene cassette (E. coli) were detected. Among the strains, no plasmid-mediated quinolone resistance [qnrA, qnrB, qnrS, qepA and aac (6 ')-Ib-cr] was found. However, two of three quinolone-resistant Klebsiella strains showed the novel amino acid substitution in the gyrA gene resulting in Ser83Asp and Asp87Glu.The clonality between E. coli isolates was also examined by pulsed-field gel electrophoresis. We consider that multidrug-resistant Gram-negative enteric bacteria in the intestinal microbiota of a cosmopolitan frog species might be a reservoir for antibiotic resistance genes.

Efforts to Identify and Combat Antimicrobial Resistance in Uganda: A Systematic Review.

The global burden of antimicrobial resistance is on the rise, resulting in higher morbidity and mortality in our communities. The spread of antimicrobial resistance in the environment and development of resistant microbes is a challenge to the control of antimicrobial resistance. Approaches, such as antimicrobial stewardship programmes and enhanced surveillance, have been devised to curb its spread. However, particularly in lower- and middle-income countries, the overall extent of antimicrobial resistance and knowledge on ongoing surveillance, stewardship or investigation efforts, are often poorly understood. This study aimed to look at the efforts that have been undertaken to detect and combat antimicrobial resistance in Uganda as a means of establishing an overview of the situation, to help inform future decisions. We conducted a systematic literature review of the PubMed database to assess these efforts. A search combining keywords associated with antimicrobial resistance were used to find relevant studies between 1995 and 2020 on surveillance of antimicrobial resistance in Uganda, and susceptibility of microbes to different drugs. The search yielded 430 records, 163 of which met the inclusion criteria for analysis. The studies were categorized according to country and region, the type of antimicrobial resistance, context of the study, study design and outcome of the study. We observed that antibacterial resistance and antimalarial resistance had the most published studies while antiviral and antifungal resistance were represented by very few studies each. Most studies were conducted in humans and hospital settings, with few in veterinary and One Health contexts, and only one that included environmental sampling. The majority of studies have focused on surveillance, susceptibility testing or resistance genes; none of our included papers had a policy or stewardship focus. The results from our work can inform public health policy on antimicrobial stewardship as it contributes to understanding the status of antimicrobial resistance surveillance in Uganda, and can also help to guide future research efforts. Notably, a One Health approach needs to be followed with respect to surveillance of antimicrobial resistance to better understand the mechanisms of resistance transfer across the human-animal–environment interface, including additional investigation in antiviral and antifungal resistance.

Antimicrobial Resistance of Escherichia coli from Retail Poultry Meats in Korea

Antimicrobial-resistant bacteria in poultry meat pose a threat to public health. This article is the first to report the prevalence of antimicrobial-resistant Escherichia coli in retail poultry meat labeled with various claims of antibiotic use in Korea. A total of 719 E. coli strains were isolated from 1,107 raw poultry (chicken and duck) meat samples purchased from nationwide retail stores between 2017 and 2019. All strains were tested for antimicrobial susceptibility with a broth microdilution method. The prevalence of antimicrobial-resistant E. coli in chicken was significantly higher than that in duck for almost all antibiotics tested, and 87.9% of E. coli strains in chicken samples were multidrug resistant. The most prevalent types of antimicrobial resistance in these E. coli strains from poultry meat were to nalidixic acid (75.7%), ampicillin (69.1%), and tetracycline (64.0%), consistent with national sales data for veterinary antibiotics in the Korean poultry production industry. Organic or antibiotic-free and conventional chicken products were equally likely to be contaminated with antimicrobial-resistant E. coli. Contamination may occur during slaughtering and subsequent processing, and antibiotic use is permitted in certain cases under organic or antibiotic-free poultry standards. Therefore, close surveillance is required throughout the chicken production chain to prevent the spread of antimicrobial-resistant E. coli strains.

Characterization of 2 Neisseria gonorrhoeae Strains With High-Level Azithromycin Resistance Isolated in 2015 and 2018 in Japan.

We identified and characterized the first 2 Neisseria gonorrhoeae strains with high-level azithromycin resistance isolated in Japan. These were in the clade of ceftriaxone- and azithromycin-resistant strains isolated in Australia and the United Kingdom. The multilocus sequence typing, N. gonorrhoeae multiantigen sequence typing, and N. gonorrhoeae sequence typing for antimicrobial resistance types of these strains were found in gonococci from eastern Asia.

Occurrence of Methicillin-Resistant Staphylococcus aureus in Ready-to-Eat Raw Fish from Japanese Cuisine Restaurants in Salvador, Brazil

The presence of methicillin-resistant Staphylococcus aureus (MRSA) strains in food products is a major issue for food safety. The present study was conducted to evaluate the occurrence and antimicrobial resistance profile of S. aureus, focusing on MRSA isolates, in ready-to-eat sashimi from Japanese restaurants in Salvador, Brazil. A total of 127 sashimi samples were collected directly from the take-out service in 16 restaurants. The staphylococcal isolates were identified morphologically and biochemically with standard laboratory procedures. S. aureus isolates were tested with a disk diffusion assay against seven antibiotics, and the cefoxitin and oxacillin were used to identify MRSA strains. Isolates with the MRSA phenotype were confirmed with a PCR assay. S. aureus was found in 73% of the sashimi samples, including sashimi from tuna (75.5% of samples) and salmon (72.5% of samples). Among those positive samples, 37% were contaminated with MRSA strains, found among 38.8% of salmon sashimi and 34.0% of tuna sashimi. Penicillin resistance was the most common type of antimicrobial resistance, found in 65.5% of the sashimi samples, followed by resistance to tetracycline (22.5%), erythromycin (16.0%), and ciprofloxacin (3.2%). Only two S. aureus isolates collected from different fish samples and restaurants had presumed resistance to vancomycin. The high prevalence of S. aureus and MRSA in these sashimi samples indicates a potential risk for foodborne disease, especially MRSA, spreading in the community.

A review on bacterial resistance to carbapenems: epidemiology, detection and treatment options.

Carbapenems are a class of antimicrobial agents reserved for infections caused by multidrug-resistant microorganisms. The emergence of carbapenem resistance has become a serious public health threat. This type of antimicrobial resistance is spreading at an alarming rate, resulting in major outbreaks and treatment failure of community-acquired and nosocomial infections caused by the clinically relevant carbapenem-producing Enterobacteriaceae or carbapenem-resistant Enterobacteriaceae. This review is focused on carbapenem resistance, including mechanisms of resistance, history and epidemiology, phenotypic and genotypic detection in the clinically relevant bacterial pathogens and the possible treatment options available.

Antimicrobial resistance patterns in Neisseria gonorrhoeae among male clients of a sexually transmitted infections clinic in Kisumu, Kenya.

Approximately 11.4 million cases of gonorrhea occur in the WHO African Region annually and global incidence has been increasing. We sought to determine the distribution and types of antimicrobial resistance in Neisseria gonorrhoeae (NG) in Kisumu, Kenya. Urethral swab specimens were obtained from men attending Universities of Nairobi, Illinois, and Manitoba sexually transmitted infection clinic with urethral discharge detected on clinical exam between 29 January and 2 July 2018. Gonorrhea was confirmed by culturing on Thayer–Martin GC Culture selective media. Disk diffusion was used to measure resistance to antimicrobials. Of the 138 males with history of urethral discharge or dysuria or urethral discharge on exam identified during the surveillance period, urethral swab samples were obtained from 60 men, and 35 (58%) were culture positive. Interpretation of the disk diffusion results showed high resistance (% of isolates) to: penicillin (97%), tetracycline (100%), ciprofloxacin (100%), and doxycycline (91%). All isolates were susceptible to ceftriaxone (100%) and azithromycin (100%). We observed high rates of resistance to several drug classes, likely driven by background selective pressure, as resistance was not observed among currently recommended Kenyan therapies for urethritis. Expanded surveillance for antimicrobial resistance in NG is warranted. Agar dilution or Etest reference testing is needed for accurate assessment of resistance.

Pandemic Bacteremic Escherichia Coli Strains: Evolution and Emergence of Drug-Resistant Pathogens.

In recent years, there have been several pandemics of E. coli strains which are highly virulent and antibiotics resistant. Here, we discuss one recent pandemic strain, ST131. These E. coli strains are members of the virulence-associated phylogenetic group B2 and exhibit extraintestinal virulence factors, including various adhesins, toxins, siderophores, and protectins. This group often also harbors a diverse range of antimicrobial resistance types and mechanisms and may have particular metabolic capacities that enable it to colonize many individuals asymptomatically, while out competing other E. coli strains. Here, we discuss this clonal group in the context of other pathogenic E. coli and focus on its specific characteristics in terms of resistance, virulence, and metabolism.

NastyBugs: A simple method for extracting antimicrobial resistance information from metagenomes

Multidrug resistant bacteria are becoming a major threat to global public health. While there are many possible causes for this, there have so far been few adequate solutions to this problem. One of the major causes is a lack of clinical tools for efficient selection of an antibiotic in a reliable way. NastyBugs is a new program that can identify what type of antimicrobial resistance is most likely present in a metagenomic sample, which will allow for both smarter drug selection by clinicians and faster research in an academic environment.

Genetic elements associated with antimicrobial resistance among avian pathogenic Escherichia coli.

BackgroundAvian-pathogenic Escherichia coli (APEC) are pathogenic strains of E. coli that are responsible for one of the most predominant bacterial disease affecting poultry worldwide called avian colibacillosis. This study describes the genetic determinants implicated in antimicrobial resistance among APEC isolated from different broiler farms in Egypt.Methods A total of 116 APEC were investigated by serotyping, antimicrobial resistance patterns to 10 antimicrobials, and the genetic mechanisms underlying the antimicrobial-resistant phenotypes.ResultsAntibiogram results showed that the highest resistance was observed for ampicillin, tetracycline, nalidixic acid, and chloramphenicol. The detected carriage rate of integron was 29.3% (34/116). Further characterization of gene cassettes revealed the presence gene cassettes encoding resistance to trimethoprim (dfrA1, dfrA5, dfrA7, dfrA12), streptomycin/spectinomycin (aadA1, aadA2, aadA5, aadA23), and streptothricin (sat2). To our knowledge, this the first description of the presence of aadA23 in APEC isolates. Analysis of other antimicrobial resistance types not associated with integrons revealed the predominance of resistance genes encoding resistance to tetracycline (tetA and tetB), ampicillin (bla TEM), chloramphenicol (cat1), kanamycin (aphA1), and sulphonamide (sul1 and sul2). Among ciprofloxacin-resistant isolates, the S83L mutation was the most frequently substitution observed in the quinolone resistance-determining region of gyrA (56.3%). The bla TEM and bla CTX−M−1 genes were the most prevalent among APEC isolates producing extended-spectrum beta-lactamase (ESβL).ConclusionsThese findings provided important clues about the role of integron-mediated resistance genes together with other independent resistance genes and chromosomal mutations in shaping the epidemiology of antimicrobial resistance in E. coli isolates from poultry farms in Egypt.