Phenotypic Resistance Profiles Research Articles

Assessment of Bacterial Contamination and Antimicrobial Resistance of Escherichia coli Isolates from Slovak Dairy Farms

The conditions in livestock housing are suitable for the survival of airborne microorganisms, mainly due to high temperatures, humidity, and the presence of organic material. The total count of airborne bacteria concentrations in cattle farms ranged from 3.01 log10 CFU/mL to 6.90 log10 CFU/mL; for coliform bacteria, they were from 2.18 log10 CFU/mL to 3.34 log10 CFU/mL; and for molds, they ranged from 3.00 log10 CFU/mL to 4.57 log10 CFU/mL. Bacteria resistant to antimicrobial substances and resistance genes can be spread on animal farms. Antimicrobial resistance in ubiquitous Escherichia coli isolated from cattle feces was investigated. Minimum inhibitory concentration (MIC) testing was utilized to identify phenotypic resistance profiles, and the PCR method was employed to detect the presence of resistant genes. A higher percentage of resistance was found to amikacin (65%), tetracycline (61%), streptomycin (56%), ampicillin (55%), and nalidixic acid (45%). Multidrug resistance was determined in up to 64.3% of the isolates studied. The most widespread resistance genes were blaTEM (85.7%), sul2 (66.7%), tetB (52.38%), and sul1 (47.6%). We found that 4.8% of the E. coli isolates had the blaCMY gene. We found that, despite phenotypic resistance, E. coli isolates do not necessarily carry genes conferring resistance to that particular antimicrobial agent.

Escherichia coli as a sentinel in the assessment of antimicrobial resistance in the tilapia production chain: from production environment to the final product

IntroductionThe intensification of tilapia production has increased animal density in tanks, leading to more frequent exposure to pathogenic agents and compromising the quality of fish products. Antimicrobial resistance is a global concern that affects human treatment, and sentinel microorganisms like Escherichia coli are crucial for monitoring production chains, especially in aquaculture, where research is still limited. The aim of this study was to identify the presence of E. coli and investigate its antimicrobial resistance profiles throughout the entire tilapia production chain.MethodsA total of 240 samples were collected from various points in the production process: carcasses before scaling (Ca), scaling wastewater (Sw), filleting wastewater (Fw), fillet washing wastewater (Tw), fillet handling surfaces (Su), and pre-packaged fillets (Pf). The samples were collected during 10 visits, each corresponding to animals from different farms. E. coli isolates were identified using MacConkey agar and biochemical tests. Phenotypic resistance profiles were determined using nine classes of antimicrobials. Extended- spectrum b-lactamase (ESBL) production was identified with ceftazidime and cefotaxime and confirmed by a double-disc synergy test. Isolates were classified as sensitive or resistant based on the inhibition zone. Multidrug-resistant (MDR) was defined as resistance to at least one agent in three or more antimicrobial categories, while extensively drug-resistant (XDR) was defined as resistance to at least one agent in all but two or fewer categories.ResultsOverall, 50.8% of the samples (122/240) tested positive for E. coli, with 403 isolates identified. Of these, 33% (133/403) were resistant to at least two antimicrobials, and 20% (48/240) of the samples had MDR isolates, with the highest frequency found at the filleting point (Fw), which also had the only XDR profile. Resistance was most commonly observed against amoxicillin (35.73%), tetracycline (30.77%), and ciprofloxacin (26.30%).DiscussionThese findings emphasize the importance of E. coli as an indicator of antimicrobial resistance throughout tilapia processing and highlight the need for good production practices and qualified technical support to mitigate risks to public health, animal health, and the environment.

A Descriptive Study on the Phenotypic Variability of Pseudomonas aeruginosa Identified by MALDI-TOF

This descriptive study investigates the phenotypic variability of 50 Pseudomonas aeruginosa colonies isolated from wastewater, identified using MALDI-TOF mass spectrometry. The contamination of wastewater by opportunistic pathogens like P. aeruginosa poses significant public health risks due to their potential to cause severe infections and contribute to the spread of antimicrobial resistance. Pseudomonas aeruginosa is particularly concerning because of its remarkable adaptability, resilience, and intrinsic and acquired antibiotic resistance mechanisms, including the production of beta-lactamases, efflux pumps, and target site mutations. Our study highlights the phenotypic diversity and antibiotic resistance profiles of P. aeruginosa strains isolated from urban and hospital environments. Using MALDI-TOF MS, we rapidly and accurately characterized these strains, providing species-level identification within minutes. This technology surpasses traditional biochemical methods in speed and accuracy, revolutionizing microbial diagnostics by offering a high-throughput, cost-effective, and reliable tool. By analyzing the phenotypic traits and resistance mechanisms of these strains, we aim to provide critical insights into their ecology and inform strategies to mitigate the risks associated with their presence in the environment. The antibiotic resistance profiles revealed varied susceptibility among the strains, with notable resistance to drugs such as erythromycin, cefoxitin, and tetracycline. The study's findings underscore the importance of integrating advanced diagnostic technologies like MALDI-TOF MS into routine environmental monitoring and public health strategies to address the challenges posed by P. aeruginosa in wastewater. Ultimately, this research contributes to understanding the dynamics of contamination and resistance in urban environments. By detailing the methodology used for the identification and characterization of the strains, as well as the results obtained, this publication aims to provide a valuable database for researchers and practitioners engaged in combating nosocomial infections and environmental pollution by P. aeruginosa. This study highlights the need for effective management measures to control the dissemination of this pathogen in aquatic systems, promoting public health and environmental safety.

A-288 Active Surveillance Cultures: Frequency of Microorganisms and Phenotypic Resistance Profile From Brazilian Public Hospitals After COVID-19 Pandemic Peak

Abstract Background Surveillance cultures are routinely used by public health authorities to screen for multidrug-resistant bacteria. Recently, the overuse of antibiotics intensified by the COVID-19 pandemic worldwide brought concerns about potential impacts on the acquisition and/or selective pressure of resistance genes, that in general carried by plasmids, which contribute to the rapid resistance spread within specific bacterial populations. The purpose of this study was to determine the prevalence of multidrug-resistant (MDR) organisms recovered from surveillance cultures (rectal, anal, nasal, and axillary) isolated from several Brazilian public hospitals. Methods Surveillance samples were analyzed from 1st January to 31st December 2023. All the swab samples were collected from patients admitted from high-risk settings or transferred from areas with high rates of MDR organisms. All clinical specimens were inoculated onto a selective media (ChromID media, bioMerieux) and incubated at 35±2°C for 18-24 h. The screening test was performed to Gram-negative bacilli (GNB) using the antibiotics ertapenem, imipenem and meropenem and for Gram-positive Cocci (GPC) screening was tested oxacillin (methicillin) and vancomycin using disc diffusion method. Bacteria identification was performed by MALDI-TOF mass spectrometry (Vitek-MS and bioMerieux) and as required, the minimal inhibitory concentrations (MIC) of antibiotics were determined using the Vitek 2 System (bioMerieux). Results A total of 71,064 rectal swab samples were processed. 4,652/71,064 (6.5%) samples showed positive results for the presence of 5.255 MDR microorganisms. Out of which, 4,477/5,255 (85.2%) were Gram-negative Bacilli (GNB) and 778/5,255 (14.8%) were Gram-positive Cocci (GPC). The majority of the isolated carbapenems resistance was Klebsiella spp. [2,791/5,255 (53.1%)], which the Klebsiella pneumoniae was the predominant species, followed by Acinetobacter baumannii [1,268/5,255 (24.1%)], Pseudomonas aeruginosa [263/5,255 (5%)], Enterobacter spp. [96/5255 (1.8%)], Serratia spp. [31/5,255 (0.6%)], Citrobacter spp. [22/5,255 (0.4%)], and others BGN [6/5,255 (0.2%)]. The resistance to vancomycin and methicillin were observed in 10% (525/5,255) of Enterococcus spp. and 4.8% (253/5,255) of Staphylococcus aureus, respectively. Conclusions The study found that K. pneumoniae carbapenem-resistant and Enterococcus spp. vancomycin-resistant were the main Gram-negative and Gram-positive organisms recovered from surveillance culture samples. However, our data draws attention to the increased cases of carbapenem-resistant Acinetobacter baumannii as the second most frequent pathogen isolated from surveillance samples after the last wave of COVID-19 pandemic. Active surveillance culture for target microorganisms followed by contact precautions to minimize the chance of transmitting MDR organisms from colonized to non-colonized patients consist of an important activity of infection control policy.

Molecular Characterization of Multidrug-Resistant Escherichia coli from Fecal Samples of Wild Animals.

Antimicrobial resistance (AMR) surveillance in fecal Escherichia coli isolates from wildlife is crucial for monitoring the spread of this microorganism in the environment and for developing effective AMR control strategies. Wildlife can act as carriers of AMR bacteria and spread them to other wildlife, domestic animals, and humans; thus, they have public health implications. A total of 128 Escherichia coli isolates were obtained from 66 of 217 fecal samples obtained from different wild animals using media without antibiotic supplementation. Antibiograms were performed for 17 antibiotics to determine the phenotypic resistance profile in these isolates. Extended-spectrum β-lactamase (ESBL) production was tested using the double-disc synergy test, and 29 E. coli strains were selected for whole genome sequencing. In total, 22.1% of the wild animals tested carried multidrug-resistant E. coli isolates, and 0.93% (2/217) of these wild animals carried E. coli isolates with ESBL-encoding genes (blaCTX-M-65, blaCTX-M-55, and blaEC-1982). The E. coli isolates showed the highest resistance rates to ampicillin and were fully susceptible to amikacin, meropenem, ertapenem, and imipenem. Multiple resistance and virulence genes were detected, as well as different plasmids. The relatively high frequency of multidrug-resistant E. coli isolates in wildlife, with some of them being ESBL producers, raises some concern regarding the potential transmission of antibiotic-resistant bacteria among these animals. Gaining insights into antibiotic resistance patterns in wildlife can be vital in shaping conservation initiatives and developing effective strategies for responsible antibiotic use.

Antimicrobial and Phylogenomic Characterization of Bacillus cereus Group Strains Isolated from Different Food Sources in Italy.

Background:Bacillus cereus is a widespread environmental Gram-positive bacterium which is especially common in soil and dust. It produces two types of toxins that cause vomiting and diarrhea. At present, foodborne outbreaks due to Bacillus cereus group bacteria (especially Bacillus cereus sensu stricto) are rising, representing a serious problem in the agri-food supply chain. Methods: In this work, we analyzed 118 strains belonging to the Bacillus cereus group, isolated from several food sources, for which in vitro and in silico antibiotic resistance assessments were performed. Results: Many strains showed intermediate susceptibility to clindamycin, erythromycin, and tetracycline, suggesting an evolving acquisition of resistance against these antibiotics. Moreover, one strain showed intermediate resistance to meropenem, an antibiotic currently used to treat infections caused by Bacillus cereus. In addition to the phenotypic antimicrobial resistance profile, all strains were screened for the presence/absence of antimicrobial genes via whole-genome sequencing. There was inconsistency between the in vitro and in silico analyses, such as in the case of vancomycin, for which different isolates harbored resistance genes but, phenotypically, the same strains were sensitive. Conclusions: This would suggest that antibiotic resistance is a complex phenomenon due to a variety of genetic, epigenetic, and biochemical mechanisms.

Antimicrobial resistance profiling of bacteria isolated from wastewater and samples of pharmaceutical industries in South India

The study was aimed to determine the phenotypic and genotypic antimicrobial resistance in the isolated bacteria from the influent (25), effluent (15), surface and ground water samples (15) surrounding the pharmaceutical industries located in south India. From 55 samples, 48 isolates of 10 different bacteria were obtained. The identified bacterial isolates were viz. Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter aerogenes, Corynebacterium sp., Acinetobacter sp., Aeromonas punctata, Ralstonia picketti, Staphylococcus aureus, Stenotrophomonas maltophillia, and Citrobacter freundii. The phenotypic profile of resistance through antibiotic susceptibility test was carried out against sixteen different antibiotics. Standard PCR technique was used for the detection of 12 resistance genes encoding carbapenems, quinoline, aminoglycoside, β-lactam belonging blaOXA-58,blaOXA-22,qnrA, qnrB, aac(6)-Ib-cr, aac (3)-XI, mec A, qepA, aadB, blaVIM, blaOXA-48 and blaNDM. Pseudomonas aeruginosa (1: TN/I/2020) showed presence of 3 resistance genes. qnrB (489 bp) gene was present in maximum of 7 isolates while blaVIM (196 bp) gene was present in 6 isolates. The resistance genes blaNDM (621 bp) was present in three different isolates; aac (X):6)-lb-cr (482 bp), qepA (495 bp), aadB (500 bp), blaOXA-58 (843 bp) resistant genes were present in two different isolates each among the bacterial isolates obtained in this study. In phenotypic resistance profiling by AST method, out of 16 antibiotics tested, 14 showed resistance. Similarly, in genotypic resistance profiling, among 12 resistance genes tested, a maximum of three resistance genes were noticed in Pseudomonas aeruginosa. There were positive and negative correlations observed between phenotypic and genotypic resistance among different antibiotics and their resistance genes indicating the variations in the resistance gene expression.

Detection and characterization of multidrug resistant Escherichia coli carrying virulence gene isolated from broilers in Bangladesh.

The emergence and dissemination of multidrug resistant (MDR) bacteria pose a severe threat to public health by limiting clinical treatment and prophylactic options. This study investigates the prevalence of Escherichia coli in broilers, their phenotypic antimicrobial resistance (AMR) profiles and the presence of virulence-associated genes (VAGs) and antimicrobial resistance genes (ARGs) using polymerase chain reaction (PCR). A total of 216 pooled cloacal samples were collected from 1080 broilers across six districts of Bangladesh. Each pooled sample comprised randomly selected cloacal swabs from five birds per farm. E. coli isolates were identified using standard bacteriological approach, followed by biochemical assays and PCR. Antimicrobial susceptibility was assessed using the Kirby-Bauer disc diffusion method, and the presence of ARGs and VAGs was determined via PCR. Five selected isolates were partially sequenced for five VAGs using Sanger sequencing. A total of 177 E. coli isolates (81.94%, 95% confidence interval: 76.24%-86.53%) were identified. The isolates showed the highest resistance to ampicillin (93.79%), followed by tetracycline (91.53%), erythromycin (89.27%) and ciprofloxacin (87%). Conversely, ceftriaxone (80.79%) showed highest susceptibility, followed by gentamicin (37.29%) and neomycin (31.07%). All isolates were MDR, with a multiple antibiotic resistance indexes were <0.3. A significant percentage (16.38%) of E. coli isolates were MDR to five antimicrobial classes and harboured blaTEM, sul1, ere (A), tetA, tetB and tetC genes. The highest prevalent ARGs were blaTEM (88.14%) followed by ere (A) (83.62%) and sul 1 (72.32%). The prevalence of VAGs was astA (56.50%), iucD (31.07%), iss (21.47%), irp2 (15.82%) and cva/cvi (3.39%), respectively. This study highlights the presence of ARGs contributing to the development of MDR in E. coli carrying VAGs in broilers. Effective monitoring and surveillance of antimicrobial usage in poultry production systems are urgently required to prevent emergence and dissemination of AMR.

Phenotypic bacterial epidemiology and antimicrobial resistance profiles in neonatal sepsis at Jimma medical center, Ethiopia: Insights from prospective study.

Epidemiological profiles and the rundown crisis of antimicrobial resistance from bacterial isolates in neonatal sepsis compel regular surveillance to enhance data-driven decision-making. Accordingly, this study aimed to assess the phenotypic epidemiology and antimicrobial resistance profiles of bacteria isolated from clinically suspected neonatal sepsis in Ethiopia. A total of 342 neonates suspected of clinical sepsis were randomly included in a prospective observational study conducted at the neonatal intensive care unit (NICU) of Jimma medical center (JMC) from May 2022 to July 2023. Blood samples were collected from each neonate and subjected to a culture test for identification of bacterial isolates and their antibiotic resistance profiles following the standardized guidelines. The laboratory results, along with relevant clinical data, were recorded using WHONET and analyzed using STATA software. Out of the 342 blood samples that were analyzed, 138 samples (40.4%, 95% CI: 35.1-45.6, P<0.01) exhibited proven bacterial infection. The infection rates were notably higher in males with 85/138 (61.6%, 95% CI: 53.4-69.8, P<0.01) and neonates aged 0-3 days with 81/138 (58.7%, 95% CI: 50.5-66.9, P<0.01). The majority of the infections were attributed to Gram-negative bacteria, accounting for 101/138(73.2%, 95% CI: 65.6-80.7) cases, with 69/101(68.3%, 95% CI: 63.8-72.8) cases involving ESBL-producing strains, while Gram-positive bacteria were responsible for 26.8% (95% CI: 19.3-34.4) of the infections. The predominant isolates included Klebsiella pneumoniae (37.7%, 95% CI: 29.6-45.8), Coagulase-negative Staphylococci (CoNs) (20.3%, 95% CI: 13.6-27.0), and Acinetobacter species (11.6%, 95% CI: 6.0-17.1). Of the total cases, 43/72 (59.7%, 95% CI: 48.4-71.1, P<0.01) resulted in mortality, with 28/72 (38.9%, 95% CI: 27.70-50.1, P<0.03) deaths linked to Extended-Spectrum Beta-Lactamase (ESBL)-producing strains. Klebsiella pneumoniae displayed high resistance rates to trimethoprim-sulfamethoxazole (100%), ceftriaxone (100%), cefotaxime (98.1%), ceftazidime (90.4%), and gentamicin (84.6%). Acinetobacter species showed resistance to ampicillin (100%), cefotaxime (100%), trimethoprim-sulfamethoxazole (75%), ceftazidime (68.8%), chloramphenicol (68.8%), and ceftriaxone (68.8%). Likewise, CoNs displayed resistance to ampicillin (100%), penicillin (100%), cefotaxime (86.0%), gentamicin (57.2%), and oxacillin (32.2%). Multidrug resistance was observed in 88.4% (95% CI: 81.8-93.0) of isolates, with ESBL-producers significantly contributing (49.3%, 95% CI: 45.1-53.5). Furthermore, 23.0% (95% CI: 15.8-31.6) exhibited a prevalent resistance pattern to seven distinct antibiotic classes. The prevalence and mortality rates of neonatal sepsis were significantly high at JMC, with a notable surge in antibiotic and multidrug resistance among bacterial strains isolated from infected neonates, specifically ESBL-producers. These resistant strains have a significant impact on infection rates and resistance profiles, highlighting the requisite for enhanced diagnostic and antimicrobial stewardship, stringent infection control, and further molecular characterization of isolates to enhance neonatal survival.

Microbiological Quality of Coconut Water Sold in the Grande Vitória Region, Brazil, and Phenogenotypic Antimicrobial Resistance of Associated Enterobacteria.

This study aimed to evaluate the microbiological quality of coconut water sold from street carts equipped with cooling coils or refrigerated at bakeries in the Grande Vitória Region, Brazil. Additionally, it assessed the phenotypic and genotypic antimicrobial resistance profiles of isolated enterobacteria. The results indicated that coconut water sold at street carts had lower microbiological quality compared to refrigerated samples, as evidenced by significantly higher counts of mesophilic microorganisms. Using MALDI-TOF, the following opportunistic pathogens were identified: Citrobacter freundii, Enterobacter bugandensis, E. kobei, E. roggenkampii, Klebsiella pneumoniae, and Kluyvera ascorbata. Three isolates-E. bugandensis, K. pneumoniae, and K. ascorbata-were classified as multidrug-resistant (MDR). Widespread resistance to β-lactams and cephalosporins was detected, and some isolates were resistant to quinolones, nitrofurans, and phosphonic acids. The gene blaCTX-M-2 was detected in C. freundii, E. bugandensis, E. kobei, and K. ascorbata. However, genes blaNDM, blaKPC, blaCMY-1, and blaCMY-2 were not detected in any isolate. The findings underscore the need to enhance good manufacturing practices in this sector to control the spread of antimicrobial resistance (AMR). To our knowledge, this is the first study documenting the presence of potentially pathogenic enterobacteria in coconut water samples and their associated phenotypic and genotypic AMR profiles.

Staphylococcus capitis: insights into epidemiology, virulence, and antimicrobial resistance of a clinically relevant bacterial species.

SUMMARYStaphylococcus capitis is divided into two subspecies, S. capitis subsp. ureolyticus (renamed urealyticus in 1992; ATCC 49326) and S. capitis subsp. capitis (ATCC 27840), and fits with the archetype of clinically relevant coagulase-negative staphylococci (CoNS). S. capitis is a commensal bacterium of the skin in humans, which must be considered an opportunistic pathogen of interest particularly as soon as it is identified in a clinically relevant specimen from an immunocompromised patient. Several studies have highlighted the potential determinants underlying S. capitis pathogenicity, resistance profiles, and virulence factors. In addition, mobile genetic element acquisitions and mutations contribute to S. capitis genome adaptation to its environment. Over the past decades, antibiotic resistance has been identified for S. capitis in almost all the families of the currently available antibiotics and is related to the emergence of multidrug-resistant clones of high clinical significance. The present review summarizes the current knowledge concerning the taxonomic position of S. capitis among staphylococci, the involvement of this species in human colonization and diseases, the virulence factors supporting its pathogenicity, and the phenotypic and genomic antimicrobial resistance profiles of this species.

In the Depths of Wash Water: Isolation of Opportunistic Bacteria from Fresh-Cut Processing Plants.

The fruit and vegetable industry in post-harvest processing plants is characterized by a substantial consumption of water resources. Wash waters may serve as an environment for the periodic or permanent habitation of microorganisms, particularly if biofilm forms on the inner walls of tanks and flushing channels. Despite the implementation of integrated food safety monitoring systems in numerous countries, foodborne pathogens remain a global public health and food safety concern, particularly for minimally processed food products such as vegetables and fruits. This necessitates the importance of studies that will explore wash water quality to safeguard minimally processed food against foodborne pathogen contamination. Therefore, the current study aimed to isolate and identify bacteria contaminating the wash waters of four fresh-cut processing plants (Poland) and to evaluate the phenotypic antibiotic resistance profiles in selected species. Bacteria were isolated using membrane filtration and identified through mass spectrometry, followed by antibiotic susceptibility testing according to EUCAST guidelines. The results revealed that the level of contamination with total aerobic bacteria in the water ranged from 1.30 × 106 cfu/mL to 2.54 × 108 cfu/mL. Among the isolates, opportunistic pathogens including Enterococcus faecalis, Pseudomonas aeruginosa, Klebsiella oxytoca, Klebsiella pneumoniae, Serratia marcescens, and Proteus vulgaris strains were identified. An especially noteworthy result was the identification of cefepime-resistant K. oxytoca isolates. These findings highlight the importance of monitoring the microbial microflora in minimally processed foods and the need for appropriate sanitary control procedures to minimize the risk of pathogen contamination, ensuring that products remain safe and of high quality throughout the supply chain.

Green synthesized silver nanoparticles from Ocimum sanctum: A potent inhibitor of biofilm forming ability and efflux pumps in bacteria causing bovine mastitis

Therapeutic management of mastitis faces significant challenges due to multidrug resistance. In the present study, multi-drug-resistant (MDR) Staphylococcus spp, Klebsiella pneumoniae, and Escherichia coli were isolated from bovine clinical mastitis cases and the phenotypic and genotypic multidrug resistance profiling was carried out. Silver nanoparticles (AgNPs) were biosynthesized using Ocimum sanctum leaf extracts and characterized via UV Vis absorption, Fourier Transform Infrared Spectroscopy, X-ray diffraction studies, Energy dispersive spectroscopy and Electron Microscopy. The determined minimum inhibitory concentration and minimum bactericidal concentration of the AgNPs against the recovered MDR isolates were 62.5 μg/ml and 125 μg/ml respectively. At a concentration of 50 μg/ml, the AgNPs demonstrated biofilm inhibitory activities of 80.35 % for MDR E. coli, 71.29 % for S. aureus and 60.18 % for MDR K. pneumoniae. Post-treatment observations revealed notable differences in biofilm formation across bacterial isolates. Furthermore, AgNP treatment led to significant downregulation of expression of the efflux pump genes acrB, acrE, acrF, and emrB in Gram-negative isolates and norB in Staphylococci isolates. This research underscores the potential for the development of an eco-friendly antimicrobial alternative in the form of green synthesized silver nanoparticles to combat drug resistance offering potential antibiofilm and efflux pump inhibitory activities.

Comparison of antimicrobial resistant Enterobacterales isolates from the dairy production environment in low and high zinc containing regions

Heavy metals occur naturally in the environment, and their concentration varies in soil across different regions. However, the presence of heavy metals may influence the antimicrobial resistance (AMR) in bacterial populations. Therefore, the objective of this study was to investigate and characterise the antimicrobial resistance profiles of Enterobacterales in soil and bovine milk filters from high and low zinc-containing regions in Ireland. In total, 50 soil samples and 29 milk filters were collected from two geographic locations with varying soil zinc concentrations. Samples were cultured for the enumeration and detection of Enterobacterales. Specifically, extended-spectrum beta-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales were isolated using selective media. Species identification was performed using MALDI-TOF. The phenotypic resistance profiles of selected Enterobacterales were determined by disk diffusion testing, following EUCAST and CLSI criteria; while, the genotypic resistance profiles of the same isolates were determined by whole genome sequencing (WGS). Heavy metal concentrations were also measured for all soil samples. A total of 40 antimicrobial resistant Enterobacterales were identified in soil (n = 31) and milk filters (n = 9). The predominant species detected in the high zinc-containing region was Escherichia coli in both sample types (soil n = 10, milk filters n = 2), while in the low zinc-containing region Serratia fonticola was predominant in soil samples (n = 8) and E. coli in milk filters (n = 4). Ten E. coli isolates identified from soil samples in the high zinc-containing region were multidrug resistant, showing resistance to all the antimicrobials tested, except for carbapenems. The WGS findings confirmed the phenotypic resistance results. Moreover, zinc resistance-associated genes and genes encoding for efflux pumps were identified. The current study revealed distinct phenotypic resistance profiles of Enterobacterales in low and high zinc-containing regions, and highlighted the benefit of utilising milk filters for AMR surveillance in dairy production.

Increasing Fluroquinolone Susceptibility and Genetic Diversity of ESBL-Producing E. coli from the Lower Respiratory Tract during the COVID-19 Pandemic.

Lower respiratory tract infections (LRTIs) are the fourth leading cause of death worldwide, among which Escherichia coli (E. coli) pneumonia is considered a rare phenomenon. Treatment options for LRTIs have become limited, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-EC), which are usually resistant to other groups of antimicrobials as well. The aim of our study was to compare the phenotypic resistance profiles and genotypes of ESBL-EC isolates associated with LRTIs before (pre-COVID-19) and during (COVID-19) the COVID-19 pandemic. All isolates were screened for antimicrobial resistance genes (ARGs) and virulence-associated genes (VAGs) and assigned to phylogenetic groups, sequence types and clonal groups by PCR. During the pandemic, a significantly lower proportion of ciprofloxacin-, levofloxacin- and trimethoprim-sulfamethoxazole-resistant ESBL-EC isolates was retrieved from lower respiratory tract (LRT) samples. PCR-based genotypization revealed greater clonal diversity and a significantly lower proportion of isolates with blaTEM, aac(6')-Ib-cr and qacEΔ1 genes. In addition, a higher proportion of isolates with the integrase gene int1 and virulence genes sat and tsh was confirmed. The lower prevalence of fluoroquinolone resistance and greater genetic diversity of ESBL-EC isolated during the COVID-19 period may have been due to the introduction of new bacterial strains into the hospital environment, along with changes in clinical establishment guidelines and practices.

Study on Antibiotic Resistance Profiles Exhibited by Vibrio Species Isolated from Landfill Soils in Zaria Metropolis, Northern Nigeria

Study’s Novelty/Excerpt This study investigates the occurrence and antibiotic resistance profiles of Vibrio species isolated from landfill soils in Zaria Metropolis, with a focus on environmental reservoirs of antibiotic resistance. The research uniquely identifies a high prevalence of Vibrio cholerae non-O1 among the isolates and reveals significant multidrug resistance (MDR), particularly against Ampicillin, while also showing complete susceptibility to Gentamicin and Chloramphenicol. These findings highlight the potential for landfills to serve as environmental reservoirs of antibiotic resistance, underscoring the need for further research to understand the implications for public health and environmental management. Full Abstract Antibiotic resistance in bacteria presents a major risk to public health and the environment. Infections caused by Vibrio species continue to be a serious public health concern. This study investigated the occurrence and antibiotic resistance profiles of Vibrio species isolates from landfill soils in Zaria Metropolis. A total of one hundred and twenty (120) soil samples were collected from designated landfills in four locations in Sabon-Gari, Samaru, Tudun-Wada, and Zaria City. Vibrio species were isolated using Thiosulphate citrate bile salt sucrose (TCBS) agar. Bacteriological analysis of the soil samples revealed 9(7.50%) Vibrio species isolates with Vibrio cholerae non-O1 exhibiting the highest prevalence of 4 (3.33%) among all isolates. Using the Kirby-Bauer method, the isolates were tested for susceptibility against ten commonly used antibiotics belonging to three different classes. The highest resistance was to Ampicillin (88. 89%), while all the isolates (100%) showed susceptibility to Gentamicin and Chloramphenicol. Five isolates (55.56%) were Multidrug Resistance (MDR). The highest Multidrug Resistance (MDR, 60%) was observed in Vibrio cholerae non-O1. The isolate resistant to the highest number of antibiotics was obtained from the Tudun-Wada sample location. Three isolates (33.33%) showed resistance to 4 antibiotics, while 2 isolates, 1(11.11%) each were resistant to 5 and 6 antibiotics. The isolates were Multiple Antibiotic Resistance (MAR) to 4-6 antibiotics, and four different phenotypic resistance profiles were observed among them. The origin and varying levels of resistance to multiple antibiotics indicated could be traced to the faecal constituent of the waste in landfills produced by people or animals that have been treated indiscriminately with various antibiotics or items containing residual antimicrobial agents disposed of in dump soils, highlighting the potential environmental reservoirs of antibiotic resistance and call for further research to understand the implications for public health and environmental management.

Widespread prevalence of plasmid-mediated blaCTX-M type extended-spectrum beta-lactamase Escherichia coli in backyard broiler production systems in the United States.

Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E. coli. Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E. coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E. coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E. coli. Assessment of ESBL phenotype was determined through using disk diffusion with 3rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E. coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a blaCTX-M gene, the dominant variant being blaCTX-M-1, and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of blaCTX-M type ESBL E. coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.

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.

Genetic Characterization and Population Structure of Drug-Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing.

The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates.

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.