Mechanisms of resistance in multiple-antibiotic-resistant Escherichia coli strains of human, animal, and food origins

Occurrence of multidrug resistant/extended spectrum beta-lactamase-producing Escherichia coli isolates belonging to high-risk clones from healthy 1-day-old broiler and layer chicks without in ovo or day-of-hatch antibiotic administration

This study aimed to investigate the presence of antimicrobial resistant Escherichia coli (E. coli) among healthy day-old broiler and layer chicks in the absence of in ovo or day-of-hatch antibiotic administration. A total of 100 pooled samples from 14 hatcheries across western Algeria were collected for analyses. Antimicrobial susceptibility testing was performed using the disc-diffusion method. Genes encoding antibiotic resistance, integrons, and phylogenetic groups were screened using Polymerase Chain Reaction (PCR), with the genetic relatedness of extended spectrum beta-lactamase (ESBL)-producing isolates determined via multilocus sequence typing. Sixty-eight samples contained E. coli, with high levels of resistance to multiple antibiotics found among broiler (92.10%) and layer chicks (100%) (no significant statistical association, P < 0.05). Multidrug-resistant (MDR)/ESBL-producing isolates were detected in samples from both broiler (n = 11) and layer (n = 2) hatcheries, from which three and five harbored blaCTX-M-1 and blaCTX-M-14, respectively. Additionally, tetA (n = 7), sul1 (n = 5), aac(6´)-Ib-cr (n = 2), and int1 (n = 7) genes were detected. Isolates belonged to the clones ST10 (n = 1), ST617 (n = 1), ST405 (n = 3), ST69 (n = 4), ST224 (n = 3), and ST4494 (n = 1). Study findings indicate that even in the absence of any prior antibiotic administration, day-old chicks in western Algerian hatcheries carry MDR isolates capable of spreading across the national poultry sector, representing a significant public health concern.

Risk for public health of multiresistant Shiga toxin-producing Escherichia coli (STEC) in wild boar (Sus scrofa) in Tunisia

BACKGROUND

Wild boar (Sus scrofa) is increasingly implicated as a reservoir of various pathogens, such as Shiga toxin-producing E. coli (STEC) that are transmissible to other wildlife, domestic animals and humans. This represents risks to both human and animal health by causing food-borne infections. This investigation set out to evaluate the antibiotic resistance profiles and virulence factor rates of STEC strains isolated from wild boars.

MATERIAL AND METHODS

A total of 110 fecal samples were taken from postmortem carcasses of wild boar that were collected during the hunting campaign. PCR was used to check for the presence of the STEC virulence genes stx1, while stx2, eaeA, and ehxA in E. coli isolates. The detection of STEC serogroups was carried out by PCR amplification. Additional virulence genes, phylogenetic groups and integrons were determined in the STEC strains. Antibiotic resistance was assessed in the isolates against 21 antimicrobial agents by disk-diffusion method.

RESULTS

STEC isolates were identified in 10.9 % (12/110) of the E. coli isolates and the serogroups were O157, O145, O45 and O26. Of the strains, 75 % contained the Shiga toxin-1 gene (stx1), stx2 and ehxA were identified in 66.7 % and 33.3 % respectively. Other virulence factors fimH, traT, iutA, cdt3, ibeA, aer and fyuA were found in 100 %, 50 %, 41.7 %, 41.7 %, 33.3 %, 25 % and 8.3 % of the strains, respectively. Integrons classes 1 and 2 were found in 58.3 % and 8.3 % of the strains, respectively. The majority of STEC isolates belonged to phylogroup B1 (58.4 %), followed by E (25 %), A (8.3 %), and D (8.3 %).

CONCLUSIONS

Our findings suggest that wild boars are an important reservoir of STEC isolates. Based on the presence of virulence factors encoding for toxins (stx1 and stx2), adhesins, and invasion among STEC strains in association with integrons as mobile genetic elements, these strains may have a high potential to cause human disease.

Impact of the Technical Snow Production Process on Bacterial Community Composition, Antibacterial Resistance Genes, and Antibiotic Input-A Dual Effect of the Inevitable

Although climate warming-induced snow cover reduction, as well as the development of ski tourism in hot and dry countries, is shifting industries toward the use of technical snowmaking, its use raises hydrological, health-related, and environmental concerns. This study was aimed at enhancing our current understanding of the impact of technical snowmaking on the environment and human health. Culturable bacteriological indicators of water quality (Escherichia coli, fecal enterococci, Salmonella, and Staphylococcus), the presence and concentration of antimicrobials, genes determining bacterial antibiotic resistance (ARGs), and next-generation sequencing-based bacterial community composition and diversity were examined from river water, technological reservoirs, and technical snow from five ski resorts. The number of culturable bacteria and prevalence of most ARGs decreased during snowmaking. The concentration of antimicrobial agents changed irregularly, e.g., ofloxacin and erythromycin dropped in the snowmaking process, while cefoxitin was quantified only in technical snow. The bacterial community composition and diversity were altered through the technical snowmaking process, resulting in the survivability of freezing temperatures or the presence of antimicrobial agents. Water storage in reservoirs prior to snowmaking allows us to reduce bacterial and ARG contaminants. Frequent and thorough cleaning of snowmaking devices may aid in reducing the negative impact snowmaking can have on the environment by reducing contaminant input and limiting the disturbance of the ecological balance.

Evaluation of multi-drug resistance, virulence factors, and antimicrobial resistance genes of non-typhoidal Salmonella isolated from ruminants as a potential human health threat in Razavi Khorasan, northeastern Iran

Non-typhoidal Salmonella (NTS) is a significant foodborne pathogen that poses a threat to human health by causing infections and potentially acquiring antibiotic resistance. We evaluated thirty-five Salmonella serovars previously isolated from cattle, sheep, goats, and their retail meat in Razavi Khorasan Province, Iran. The isolates were confirmed with Salmonella polyvalent antiserum. Furthermore, PCR was used to identify the Salmonella Enteritidis, Salmonella Typhimurium, and the host-adapted serovars Salmonella Dublin and Salmonella Abortusovis. Additionally, the antimicrobial susceptibility of the serovars was evaluated using the disk diffusion method. Subsequently, the occurrence of antimicrobial resistance genes and virulence factors was evaluated using the PCR technique. Molecular typing revealed that 20 % of the isolates were S. Typhimurium, 11.4 % were S. Dublin, 8.6 % were S. Enteritidis, 5.7 % were S. Abortusovis, and 54.3 % (19 isolates) were classified as non-typed serovars. Salmonella isolates showed high susceptibility to ciprofloxacin (91.4 %), colistin (88.6 %), gentamicin (88.6 %), and cefotaxime (85.7 %) while exhibiting high resistance to others such as ampicillin (88.6 %), streptomycin (74.3 %), and tetracycline (51.4 %). The most prevalent resistance genes in non-typhoidal Salmonella (NTS) are blaTEM (91.4 %), sul1 (65.7 %), and aadA (54.3 %). Additionally, twenty-five isolates (71.4 %) showed multi-drug resistance profiles. The most frequent virulence genes are stn (100 %), iroN (100 %), and pefA (42.9 %). The current study has revealed that Salmonella serovars isolated from sheep and goats, like those from cattle, exhibit multi-drug resistance and harbor antimicrobial resistance genes. Additionally, they possess diverse virulence factors that can threaten human health by spreading diseases and developing drug resistance, leading to antibiotic treatment failure.

Assessment of Antibiotic Resistance Among Isolates of Klebsiella spp. and Raoultella spp. in Wildlife and Their Environment from Portugal: A Positive Epidemiologic Outcome

One of the significant challenges facing modern medicine is the rising rate of antibiotic resistance, which impacts public health, animal health, and environmental preservation. Evaluating antibiotic resistance in wildlife and their environments is crucial, as it offers essential insights into the dynamics of resistance patterns and promotes strategies for monitoring, prevention, and intervention. Klebsiella and Raoultella genera isolates were recovered from fecal samples of wild animals and environmental samples using media without antibiotic supplementation. Antibiograms were performed for 15 antibiotics to determine the phenotypic resistance profile in these isolates. Extended-spectrum β-lactamase (ESBL) production was tested by the double-disc synergy test, and one ESBL-producing K. pneumoniae isolate was screened by PCR and whole-genome sequencing. Biofilm production was analyzed using the microtiter plate method. A total of 23 Klebsiella spp. and 3 Raoultella spp. isolates were obtained from 312 fecal samples from wild animals, 9 Klebsiella spp. and 4 Raoultella spp. isolates were obtained from 18 river and stream water samples, and 4 Klebsiella spp. and 3 Raoultella spp. isolates from 48 soil samples. Regarding antibiotic resistance, only one isolate of K. pneumoniae from soil samples was an ESBL-producer and showed resistance to six antibiotics. This isolate harbored multiple β-lactams genes (blaCTX-M-15, blaTEM-1, blaSHV-28, and blaOXA-1), as well as genes of resistance to quinolones, sulfonamides, tetracycline, aminoglycosides, and chloramphenicol, and belonged to the lineage ST307. Most of the Klebsiella spp. and Raoultella spp. isolates were biofilm producers (except for one Klebsiella isolate), and 45.6% were weak biofilm producers, with the remaining being moderate to strong biofilm producers. We can conclude that antibiotic resistance is not widespread in these environment-associated isolates, which is a positive epidemiological outcome. However, identifying a single ESBL-K. pneumoniae isolate should serve as a warning of potential hotspots of resistance emergence.

Screening and Identification of Natural Compounds as Potential Inhibitors of Glutamate Racemase, an Emerging Drug Target of Food Pathogen E. coli O157:H7: An In-silico Approach to Combat Increasing Drug Resistance

BACKGROUND

Shiga Toxin-Producing Escherichia coli (E. coli) O157:H7, capable of causing serious food-borne illnesses, is extensively studied and is known to be transmitted through animal reservoirs or person-to-person contact, leading to severe disease outbreaks. The emergence of antibiotic resistance in these strains, coupled with increased adverse effects of existing therapeutics, underscores the urgent need for alternative therapeutic strategies.

OBJECTIVE

This study aims to evaluate Glutamate Racemase (MurI protein) of the food-pathogenic E. coli O157:H7 (EC MurI) as a novel drug target. Furthermore, the study seeks to identify new compounds with potential inhibitory effects against this protein.

METHODS

Using computational tools, the study identified inhibitor binding sites on EC MurI and identified relevant inhibitors capable of binding to these sites. Molecular docking techniques were employed to assess potential hits, and selected compounds were further analyzed for their structural activity and binding affinity to the protein.

RESULTS

The results of the study revealed that Frigocyclinone and Deslanoside, exhibited the best binding affinity with EC-MurI. Subsequent molecular dynamic (MD) simulations of the selected complexes indicated that both compounds were stable. This suggests that Frigocyclinone and Deslanoside have the potential to serve as potent inhibitors of EC-MurI.

CONCLUSION

In summary, this study highlights the urgent need for alternative therapies against food-pathogenic E. coli, focusing on E. coli O157:H7. Evaluation of Glutamate Racemase as a drug target identified Frigocyclinone and Deslanoside as promising inhibitors. MD simulations indicated their stability, suggesting their potential as lead molecules for further research and treatment development.

Dairy Cattle and the Iconic Autochthonous Cattle in Northern Portugal Are Reservoirs of Multidrug-Resistant Escherichia coli

Background/Objectives: Animals destined for human consumption play a key role in potentially transmitting bacteria carrying antibiotic resistance genes. However, there is limited knowledge about the carriage of antibiotic-resistant bacteria in native breeds. We aimed to characterize the phenotypic profiles and antibiotic resistance genes in Escherichia coli isolated from bovines, including three native Portuguese bovine breeds. Methods: Forty-nine E. coli isolates were selected from 640 fecal samples pooled by age group (eight adult or eight calf samples) from each farm, representing both dairy cattle raised in intensive systems and meat cattle raised in extensive systems in Northern Portugal. The presumptive E. coli colonies plated onto MacConkey agar were confirmed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). The antibiotic resistance profiles were screened by antimicrobial susceptibility testing (EUCAST/CLSI guidelines), and the antibiotic resistance genes by PCR. Results: Most isolates showed resistance to ampicillin (69%), tetracycline (57%), gentamicin (55%), and trimethoprim + sulfamethoxazole (53%), with no resistance to imipenem. Resistance to at least one antibiotic was found in 92% of isolates, while 59% exhibited multidrug resistance. Most calf isolates, including those from native breeds, showed a multidrug-resistant phenotype. Among the adults, this was only observed in Holstein-Friesian and Barrosã cattle. None of the Holstein-Friesian isolates were susceptible to all the tested antibiotics. ESBL-producing E. coli was identified in 39% of isolates, including those from Holstein-Friesian calves and adults, Cachena calves and Minhota adults. The sul2 gene was detected in 69% of isolates, followed by blaCTX-M (45%), aac(3')-IV (41%), and aac(6')-Ib-cr (31%), with a higher prevalence in adults. Conclusions: This pioneering study highlights the concerning presence of multidrug-resistant E. coli in native Portuguese cattle breeds.

Occurrence, antibiotic resistance and molecular characterisation of Shiga toxin-producing Escherichia coli isolated from broiler chickens in Tunisia

1. Shiga toxin-producing Escherichia coli (STEC) strains are associated with disease outbreaks which cause a public health problem. The aim of this study was to determine the frequency of STEC strains, their virulence factors, phylogenetic groups and antimicrobial resistance profiles in broiler chickens.2. A total of 222 E.coli isolates were collected from the caecum of chickens intended to be slaughtered. Antibiotic susceptibility was tested against 21 antimicrobial agents and ESBL phenotype was assessed by double-disk synergy test. The presence of STEC virulence genes stx1, stx2,eaeA and ehxA was detected by PCR. The identification of STEC serogroups was realised by PCR amplification. Additive virulence genes, phylogenetic groups and integrons were examined among the STEC isolates.3. Out of 222 E.coli isolates, 72 (32%) were identified as STEC strains and the most predominant serogroups were O103, O145 and O157. Shiga toxin gene 1 (stx1) was found in 84.7% (61/72) of the STEC strains, and eae and stx2 were detected in 38.8% and 13.8%, respectively. The ESBL phenotype was documented in 48.6% (35/72) of isolates. Most of the isolates (90.3%) carried class 1 integron with the gene cassette encoding resistance to trimethoprim (dfrA) and streptomycin (aadA) in 31.9% of the isolates. Class 2 integron was identified in 36.1% of isolates.4. Broilers can be considered as a reservoir of STEC strains which have high virulence factors and integrons that might be transmitted to other chickens, environments and humans. It is important to undertake surveillance and efficient control measures in slaughterhouses and farms to control measures of STEC bacteria.

Escherichia coli Occurrence and Antimicrobial Resistance in a Swine Slaughtering Process

The swine production chain can be a reservoir of antimicrobial-resistant Escherichia coli, which transfers resistance genes to other bacteria, serving as an important biomarker in the One Health approach. This study aimed to identify the frequency and antimicrobial resistance profile of E. coli in the swine production chain, assess the presence of extended-spectrum beta-lactamases (ESBL), and compare resistance profiles across different sample types. A total of 622 samples of swine carcasses from various points of the slaughter process (n = 400), swine feces (n = 100), commercial cuts (n = 45), environment (n = 67), and feces from employees (n = 10) of a pig slaughterhouse certified by the Federal Inspection Service, located in São Paulo state, Brazil, were collected. A total of 1260 E. coli isolates were obtained from the samples, with 73.6% of the samples testing positive. The agar disk diffusion test was performed with 10 different classes of antimicrobials. To confirm the production of ESBLs, the isolates were submitted to a double-disk synergism test using cefotaxime, ceftazidime, and amoxicillin with clavulanic acid. Of the total isolates, 80.71% were multidrug resistant. All ESBL-producing isolates were multidrug resistant and resistant to amoxicillin, tetracycline, and chloramphenicol. Isolates from human feces samples had less chance of being multidrug resistant than samples from other sources. The diversity of resistance profiles was verified in the samples, not clustering according to the sources, except for human feces isolates that clustered, evidencing lower antimicrobial resistance variability of these samples. Antimicrobial resistance is significantly present in the pork production chain, necessitating a comprehensive multidisciplinary approach to effectively mitigate risks within the One Health framework.

Nanocomposites: silver nanoparticles and bacteriocins obtained from lactic acid bacteria against multidrug-resistant Escherichia coli and Staphylococcus aureus

Drug-resistant bacteria such as Escherichia coli and Staphylococcus aureus represent a global health problem that requires priority attention. Due to the current situation, there is an urgent need to develop new, more effective and safe antimicrobial agents. Biotechnological approaches can provide a possible alternative control through the production of new generation antimicrobial agents, such as silver nanoparticles (AgNPs) and bacteriocins. AgNPs stand out for their antimicrobial potential by employing several mechanisms of action that can act simultaneously on the target cell such as the production of reactive oxygen species and cell wall rupture. On the other hand, bacteriocins are natural peptides synthesized ribosomally that have antimicrobial activity and are produced, among others, by lactic acid bacteria (LAB), whose main mechanism of action is to produce pores at the level of the cell membrane of bacterial cells. However, these agents have disadvantages. Nanoparticles also have limitations such as the tendency to form aggregates, which decreases their antibacterial activity and possible cytotoxic effects, and bacteriocins have a narrow spectrum of action, require high doses to be effective, and can be degraded by proteases. Given these limitations, nanoconjugates of these two agents have been developed that can act synergistically in the control of pathogenic bacteria resistant to antibiotics. This review focuses on knowing relevant aspects of the antibiotic resistance of E. coli and S. aureus, the characteristics of these new generation antibacterial agents, and their effect alone or forming nanoconjugates that are more effective against the multiresistant mentioned bacteria.

Extended-spectrum beta-lactamase (ESBL)- and non-ESBL producing Escherichia coli surveillance in surface water sources in Edo State, Nigeria: a public health concern

This research explores the antimicrobial resistance (AMR) profiles and prevalence of extended-spectrum beta-lactamase (ESBL) and non-ESBL-producing Escherichia coli in Ojerame Dam and Ovokoto Spring, Edo State, Nigeria. Over 12 months, water was systematically sampled to accommodate seasonal variations and analyzed by employing an ESBL-selective medium for bacterial species. Additionally, bacterial isolates underwent identification and characterization using polymerase chain reaction (PCR) and disk diffusion methods to evaluate their susceptibility to antimicrobials. Results indicated significant prevalence of ESBL-producing E. coli, which exhibited complete resistance to common antimicrobials like ceftriaxone, ceftazidime, cefotaxime, and ampicillin while demonstrating 100% sensitivity to ertapenem, imipenem, meropenem, and nitrofurantoin. Non-ESBL-producing E. coli were resistant to ampicillin but sensitive to other antimicrobials mentioned earlier. Furthermore, both ESBL and non-ESBL-producing E. coli displayed multidrug resistance to varying degrees. Specific ESBL genes, including blaTEM, blaCTX-M-1, and blaCTX-M-15, were identified, alongside resistance genes like tetA, tetM, sul1, sul2, sul3, qnrA, qnrB, and qnrS in E. coli. This study pioneers the documentation of ESBL-producing E. coli in surface water in the region. This signals impending health risks associated with water being a reservoir of resistant genes while emphasizing the urgency for further research and public awareness concerning the quality of surface water.

Emergence of Salmonella Infantis carrying the pESI-like plasmid from eggs in egg grading and packing plants in Korea

The plasmid of emerging S. Infantis (pESI) or pESI-like plasmid in Salmonella enterica Infantis are consistently reported in poultry and humans worldwide. However, there has been limited research on these plasmids of S. Infantis isolated from eggs. Therefore, this study aimed to analyze the prevalence and characteristics of S. Infantis carrying the pESI-like plasmid from eggs in egg grading and packing plants. In this study, the pESI-like plasmid was only detected in 18 (78.3%) of 23 S. Infantis isolates, and it was absent in the other 9 Salmonella serovars. In particular, S. Infantis isolates carrying the pESI-like plasmid showed the significantly higher resistance to β-lactams, phenicols, cephams, aminoglycosides, quinolones, sulfonamides, and tetracyclines than Salmonella isolates without the pESI-like plasmid (p < 0.05). Moreover, all S. Infantis isolates carrying the pESI-like plasmid were identified as extended-spectrum β-lactamase (ESBL) producer, harboring the blaCTX-M-65 and blaTEM-1 genes, and carried non-β-lactamase resistance genes (ant(3'')-Ia, aph(4)-Ia, aac(3)-IVa, aph(3')-Ic, sul1, tetA, dfrA14, and floR) against five antimicrobial classes. However, all isolates without the pESI-like plasmid only carried the blaTEM-1 gene among the β-lactamase genes, and either had no non-β-lactamase resistance genes or harbored non-β-lactamase resistance genes against one or two antimicrobial classes. Furthermore, all S. Infantis isolates carrying the pESI-like plasmid carried class 1 and 2 integrons and the aadA1 gene cassette, but none of the other isolates without the pESI-like plasmid harbored integrons. In particular, D87Y substitution in the gyrA gene and IncP replicon type were observed in all the S. Infantis isolates carrying the pESI-like plasmid but not in the S. Infantis isolates without the pESI-like plasmid. The distribution of pulsotypes between pESI-positive and pESI-negative S. Infantis isolates was clearly distinguished, but all S. Infantis isolates were classified as sequence type 32, regardless of whether they carried the pESI-like plasmid. This study is the first to report the characteristics of S. Infantis carrying the pESI-like plasmid isolated from eggs and can provide valuable information for formulating strategies to control the spread of Salmonella in the egg industry worldwide.

Antibiotic resistance of Escherichia coli isolated from food and clinical environment in China from 2001 to 2020

Antibiotics are widely used in China's aquaculture, agricultural, and clinical settings and can lead to antibiotic resistance in various pathogens. Although the pooled prevalence estimate (PPE) and antibiotic resistance of Escherichia coli (E. coli) in food and clinical settings has been extensively studied, a comprehensive analysis of the published literature is lacking. We conducted a comprehensive search for research indicators for 2001-2020 in eight major Chinese and English literature databases. Antibiotic PPE and resistance trends of 5933 and 29,451 E. coli isolates were screened and analysed in 35 food studies (total 1821) and 62 clinical studies (total 5159). E. coli strains derived from food had the highest antibiotic resistance rate to tetracycline (TET, 71.3 %), followed by trimethoprim-sulfamethoxazole (SXT, 62.5 %) and cefazolin (CFZ, 36.2 %). E. coli strains isolated from clinical environments were highly resistant to piperacillin (PIP, 71.7 %), TET (68.3 %) and CFZ (60.9 %), consistent with foodborne E. coli drug resistance patterns. E. coli strains isolated from food and clinical samples collected in laboratories carry multiple antibiotic resistance genes (ARGs), such as blaTEM, gryA, gryB, sul1, and tetA, making E. coli a reservoir of ARGs. This study highlights the presence of drug-resistant E. coli pathogens and ARGs in food and clinical environments.

Analysis of in vitro expression of virulence genes related to antibiotic and disinfectant resistance in Escherichia coli as an emerging periodontal pathogen

The collective involvement of virulence markers of Escherichia coli as an emerging pathogen associated with periodontitis remains unexplained. This study aimed to implement an in vitro model of infection using a human epithelial cell line to determine the virulome expression related to the antibiotic and disinfectant resistance genotype and pulse field gel electrophoresis (PFGE) type in E. coli strains isolated from patients with periodontal diseases. We studied 100 strains of E. coli isolated from patients with gingivitis (n = 12), moderate periodontitis (n = 59), and chronic periodontitis (n = 29). The identification of E. coli and antibiotic and disinfectant resistance genes was performed through PCR. To promote the expression of virulence genes in the strains, an in vitro infection model was used in the human epithelial cell line A549. RNA was extracted using the QIAcube robotic equipment and reverse transcription to cDNA was performed using the QuantiTect reverse transcription kit (Qiagen). The determination of virulence gene expression was performed through real-time PCR. Overall, the most frequently expressed adhesion genes among the isolated strains of gingivitis, moderate periodontitis, and chronic periodontitis were fimH (48%), iha (37%), and papA (18%); those for toxins were usp (33%); those for iron acquisition were feoB (84%), fyuA (62%), irp-2 (61%), and iroN (35%); those for protectins were traT (50%), KpsMT (35%), and ompT (28%); and those for pathogenicity islands were malX (45%). The most common antibiotic and disinfectant resistance genes among gingivitis, moderate periodontitis, and chronic periodontitis strains were sul-2 (43%), blaSHV (47%), blaTEM (45%), tet(A) (41%), dfrA1 (32%), marR-marO (57%), and qacEA1 (79%). The findings revealed the existence of a wide distribution of virulome expression profiles related to the antibiotic and disinfectant resistance genotype and PFGE type in periodontal strains of E. coli. These findings may contribute toward improving the prevention and treatment measures for periodontal diseases associated with E. coli.

Surveillance of Enterobacteriaceae from Diabetic Foot Infections in a Tunisian Hospital: Detection of E. coli-ST131-blaCTX-M-15 and K. pneumoniae-ST1-blaNDM-1 Strains

The study determined the prevalence, antimicrobial resistant (AMR) determinants, and genetic characteristics of Escherichia coli and Klebsiella pneumoniae isolates from patients with diabetic foot infection (DFI) in a Tunisian hospital. A total of 26 Escherichia spp. and Klebsiella spp. isolates were recovered and identified by MALDI-TOF-MS. Antimicrobial susceptibility testing, the detection of AMR determinants and Shiga-like toxin genes, phylogenetic grouping, and molecular typing were performed. Twelve E. coli, 10 K. pneumoniae, 3 K. oxytoca, and 1 E. hermanii were isolated. A multidrug-resistant phenotype was detected in 65.4% of the isolates. About 30.8% of isolates were extended-spectrum β-lactamase (ESBL) producers and mainly carried blaCTX-M-15 and blaCTX-M-14 genes. One blaNDM-1-producing K. pneumoniae-ST1 strain was identified. Class 1 integrons were detected in 11 isolates and 5 gene cassette arrangements were noted: dfrA1+aadA1 (n = 1), dfrA12+aadA2 (n = 3), and dfrA17+aadA5 (n = 1). Other non-β-lactam resistance genes detected were as follows (number of isolates): aac(3')-II (3), aac(6')-Ib-cr(8), qnrB (2), qnrS (4), cmlA (2), floR (4), sul1 (11), sul2 (11), and sul3 (2). The phylogroup B1 was the most frequent (41.7%) among E. coli, and two ESBL-producing isolates corresponded to the ST131-B2 lineage. The ESBL- and carbapenemase-producing Enterobacteriaceae in DFIs are described for the first time in Tunisia.

Prevalence and characterization of quinolone resistance and integrons in clinical Gram-negative isolates from Gaza strip, Palestine

BACKGROUND

Gram-negative bacteria with quinolone resistance and extended-spectrum beta-lactamases (ESBLs) present significant treatment challenges. This study evaluated the prevalence and characteristics of quinolone resistance in Gram-negative strains, investigating the relationship between plasmid-mediated quinolone resistance (PMQR), ESBLs, and integrons.

METHODS AND RESULTS

We collected 146 Gram-negative isolates from patients in three Palestinian hospitals. For quinolone resistance isolates, the presence and characterization of PMQR, β-lactamase genes and integrons were studied by PCR and sequencing. Out of 146 clinical isolates, 64 (43.8%) were resistant to quinolones, with 62 (97%) being multidrug-resistant (MDR) and 33 (51.5%) ESBL-producers. PMQR-encoding genes were present in 45 (70.3%) isolates, including aac(6')-Ib-cr (26.6%), qnrA (18.8%), qnrS1 (20.8%), and qnrB (6.4%). BlaCTX-M genes were detected in 50% (32/64) of isolates, with blaCTX-M-15 being the most common. BlaTEM-1, blaSHV-1 and blaVIM genes were found in 13, 6, and 4 isolates, respectively. Class I integrons were found in 31/64 (48%) of isolates, with 14 containing gene cassettes conferring resistance to trimethoprim (dhfr17, dfrA12, dfrA1) and aminoglycosides resistance genes (aadA1, aadA2, aadA5, and aadA6).

CONCLUSIONS

This study found a high rate of quinolone resistance, ESBL and integrons in clinical Gram-negative isolates from our hospitals. Urgent measures are crucial, including implementing an antimicrobial resistance surveillance system, to control and continuously monitor the development of antimicrobial resistance.

Differences of Escherichia coli isolated from different organs of the individual sheep: molecular typing, antibiotics resistance, and biofilm formation

Despite numerous studies on Escherichia coli (E. coli) from sheep, there have been few reports on the characterization of E. coli isolates from various organs of individual sheep until now. The present study conducted molecular typing, antibiotics resistance, biofilm formation, and virulence genes on E. coli isolated from 57 freshly slaughtered apparently healthy sheep carcasses, gallbladders, fecal samples, and mesenteric lymph nodes (MLNs). The results demonstrated that the detection rate of R1 LPS core type in E. coli isolated from fecal samples (70.83%) was higher than that from other organs, but the detection rate of antibiotic resistance genes was lower (P < 0.05). The predominant phylogenetic group of E. coli isolated from the carcasses was group B1 (93.33%), and the detection rate of multidrug-resistance phenotype (80%) and the resistance rate of E. coli was higher than that from other organs (P < 0.05). Interestingly, the intensity of biofilm formation of E. coli isolated from MLNs was higher than that from other organs (P < 0.05). However, except for ibeB, the detection rates of virulence genes did not differ in E.coli isolated from different organs. In conclusion, differences were noted in these parameters of E. coli isolated from different organs of individual sheep. Therefore, the data may contain considerable mistakes concerning the actual situation in the host if we only analyze the data of E. coli isolated from feces or carcasses.

Variations in antimicrobial resistance genes present in the rectal faeces of seals in Scottish and Liverpool Bay coastal waters

Antibiotic resistance genes originating from human activity are considered important environmental pollutants. Wildlife species can act as sentinels for coastal environmental contamination and in this study we used qPCR array technology to investigate the variety and abundance of antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs) and integrons circulating within seal populations both near to and far from large human populations located around the Scottish and northwest English coast. Rectal swabs were taken from 50 live grey seals and nine live harbour seals. Nucleic acids were stabilised upon collection, enabling extraction of sufficient quality and quantity DNA for downstream analysis. 78 ARG targets, including genes of clinical significance, four MGE targets and three integron targets were used to monitor genes within 22 sample pools. 30 ARGs were detected, as well as the integrons intl1 and intl2 and tnpA transposase. Four β-lactam, nine tetracycline, two phenicol, one trimethoprim, three aminoglycoside and ten multidrug resistance genes were detected as well as mcr-1 which confers resistance to colistin, an important drug of last resort. No sulphonamide, vancomycin, macrolide, lincosamide or streptogramin B (MLSB) resistance genes were detected. Resistance genes were detected in all sites but the highest number of ARGs (n = 29) was detected in samples derived from grey seals on the Isle of May, Scotland during the breeding season, and these genes also had the highest average abundance in relation to the 16S rRNA gene. This pilot study demonstrates the effectiveness of a culture-independent workflow for global analysis of ARGs within the microbiota of live, free-ranging, wild animals from habitats close to and remote from human habitation, and highlights seals as a valuable indicator species for monitoring the presence, abundance and land-sea transference of resistance genes within and between ecosystems.

The Prevalence of Antibiotic Resistance Phenotypes and Genotypes in Multidrug-Resistant Bacterial Isolates from the Academic Hospital of Jaén, Spain

The heterogenicity of antimicrobial resistance genes described in clinically significant bacterial isolates and their potential role in reducing the efficacy of classically effective antibiotics pose a major challenge for global healthcare, especially in infections caused by Gram-negative bacteria. We analyzed 112 multidrug-resistant (MDR) isolates from clinical samples in order to detect high resistance profiles, both phenotypically and genotypically, among four Gram-negative genera (Acinetobacter, Escherichia, Klebsiella, and Pseudomonas). We found that 9.8% of the total selected isolates were classified as extensively drug-resistant (XDR) (six isolates identified as A. baumannii and five among P. pneumoniae isolates). All other isolates were classified as MDR. Almost 100% of the isolates showed positive results for blaOXA-23 and blaNDM-1 genes among the A. baumannii samples, one resistance gene (blaCTX-M) among E. coli, and two genetic determinants (blaCTX-M and aac(6')-Ib) among Klebsiella. In contrast, P. aeruginosa showed just one high-frequency antibiotic resistance gene (dfrA), which was present in 68.42% of the isolates studied. We also describe positive associations between ampicillin and cefotaxime resistance in A. baumannii and the presence of blaVEB and blaGES genes, as well as between the aztreonam resistance phenotype and the presence of blaGES gene in E. coli. These data may be useful in achieving a better control of infection strategies and antibiotic management in clinical scenarios where these multidrug-resistant Gram-negative pathogens cause higher morbidity and mortality.

Unexpected role of pig nostrils in the clonal and plasmidic dissemination of extended-spectrum beta-lactamase-producing Escherichia coli at farm level

The presence of methicillin-resistant or -susceptible S. aureus in pig nostrils has been known for a long time, but the occurrence of extended-spectrum beta-lactamase (ESBL)-producing E. coli has hardly been investigated. Here, we collected 25 E. coli recovered from nasal samples of 40 pigs/10 farmers of four farms. Nine ESBL-producing isolates belonging to ST48, ST117, ST847, ST5440, ST14914 and ST10 were retrieved from seven pigs. All blaESBL genes (blaCTX-M-32,blaCTX-M-14,blaCTX-M-1,blaCTX-M-65, and blaSHV-12) were horizontally transferable by conjugation through plasmids belonging to IncI1 (n=3), IncX1 (n=3) and IncHI2 (n=1) types. IncI1-plasmids displayed different genetic environments: i) IS26-blaSHV-12-deoR-IS26, ii) wbuC-blaCTX-M-32-ISKpn26 (IS5), and iii) IS930-blaCTX-M-14-IS26. The IncHI2-plasmid contained the genetic environment IS903-blaCTX-M-65-fipA with multiple resistance genes associated either to: a) Tn21-like transposon harbouring genes conferring aminoglycosides/beta-lactams/chloramphenicol/macrolides resistance located on two atypical class 1 integrons with an embedded ΔTn5393; or b) Tn1721-derived transposon displaying an atypical class 1 integron harbouring aadA2-arr3-cmlA5-blaOXA-10-aadA24-dfrA14, preceding the genetic platform IS26-blaTEM-95-tet(A)-lysR-floR-virD2-ISVsa3-IS3075-IS26-qnrS1, as well as the tellurite resistance module. Other plasmids harbouring clinically relevant genes were detected, such as a ColE-type plasmid carrying the mcr-4.5 gene. Chromosomally encoded genes (fosA7) or integrons (intI1-dfrA1-aadA1-qacE-sul1/intI1-IS15-dfrA1-aadA2) were also identified. Finally, an IncY plasmid harbouring a class 2 integron (intI2-dfrA1-sat2-aadA1-qacL-IS406-sul3) was detected but not associated with a blaESBL gene. Our results evidence that pig nostrils might favour the spread of ESBL-E. coli and mcr-mediated colistin-resistance. Therefore, enhanced monitoring should be considered, especially in a sector where close contact between animals in intensive farming increases the risk of spreading antimicrobial resistance.

Multidrug resistance in pathogenic Escherichia coli isolates from urinary tract infections in dogs, Spain

Escherichia coli (E. coli) is a pathogen frequently isolated in cases of urinary tract infections (UTIs) in both humans and dogs and evidence exists that dogs are reservoirs for human infections. In addition, E. coli is associated to increasing antimicrobial resistance rates. This study focuses on the analysis of antimicrobial resistance and the presence of selected virulence genes in E. coli isolates from a Spanish dog population suffering from UTI. This collection of isolates showed an extremely high level of phenotypic resistance to 1st-3rd generation cephalosporins, followed by penicillins, fluoroquinolones and amphenicols. Apart from that, 13.46% of them were considered extended-spectrum beta-lactamase producers. An alarmingly high percentage (71.15%) of multidrug resistant isolates were also detected. There was a good correlation between the antimicrobial resistance genes found and the phenotypic resistance expressed. Most of the isolates were classified as extraintestinal pathogenic E. coli, and two others harbored virulence factors related to diarrheagenic pathotypes. A significant relationship between low antibiotic resistance and high virulence factor carriage was found, but the mechanisms behind it are still poorly understood. The detection of high antimicrobial resistance rates to first-choice treatments highlights the need of constant antimicrobial resistance surveillance, as well as continuous revision of therapeutic guidelines for canine UTI to adapt them to changes in antimicrobial resistance patterns.

Characteristics, Whole-Genome Sequencing and Pathogenicity Analysis of Escherichia coli from a White Feather Broiler Farm

Avian colibacillosis, caused by avian Escherichia coli (E. coli), has historically been one of the most prevalent infectious diseases in large-scale poultry production, causing growth delays and mortality in chickens, resulting in huge economic losses. In recent years, the widespread use of antibiotics has led to the emergence of multidrug resistance in E. coli as a significant global problem and long-term challenge. Resistant E. coli can be transmitted to humans through animal products or the environment, which presents significant public health concerns and food safety issues. In this study, we analyzed the features of 135 E. coli strains obtained from a white feather broiler farm in Shandong, China, including antimicrobial susceptibility tests, detection of class 1 integrons, drug resistance genes, virulence genes, and phylogenetic subgroups. It is particularly worrying that all 135 E. coli strains were resistant to at least five antibiotic agents, and 100% of them were multidrug-resistant (MDR). Notably, the resistance genes of blaTEM, blaCTX-M, qnrS, aaC4, tetA, and tetB exhibited a high prevalence of carriage among the tested resistance genes. However, mcr-2~mcr-9 were not detected, while the prevalence of mcr-1 was found to be 2.96%. The most common virulence genes detected were EAST1 (14.07%, encoding enterotoxins) and fyuA (14.81%, encoding biofilm formation). Phylogenetic subgroup analysis revealed that E. coli belonging to groups B2 and D, which are commonly associated with high virulence, constituted 2.22% and 11.11%, respectively. The positive rate of class 1 integrons was 31.1%. Whole-genome sequencing (WGS) and animal experiments were performed on a unique isolated strain called 21EC78 with an extremely strong membrane-forming capacity. The WGS results showed that 21EC78 carried 11 drug resistance genes and 16 virulence genes. Animal experiments showed that intraperitoneal injection with 2 × 105 CFU could cause the death of one-day-old SPF chickens in 3 days. However, the mortality of Luhua chickens was comparatively lower than that of SPF chickens. This study reports the isolation of multidrug-resistant E. coli strains in poultry, which may pose a potential threat to human health via the food chain. Furthermore, the findings of this study enhance our comprehension of the frequency and characteristics of multidrug-resistant E. coli in poultry farms, emphasizing the urgent need for improved and effective continuous surveillance to control its dissemination.

Antimicrobial resistance in E. Coli of animal origin and discovery of a novel ICE mobile element in Northeast China

BACKGROUND

Multidrug resistance in Enterobacteriaceae including resistance to quinolones is rising worldwide. The development of resistance may lead to the emergence of new transmission mechanisms. In this study, the collection of different E. coli was performed from animals and subjected to subsequent procedures including pulsed-field gel electrophoresis, micro-broth dilution method, polymerase chain reaction. Whole genome sequencing of E. coli C3 was performed to detect the affinity, antimicrobial resistance and major carriers of the isolates.

RESULTS

A total of 66 E. coli were isolated and their antibiotic resistance genes, frequency of horizontal transfer and genetic environment of E. coli C3 were determined. The results showed there were both different and same types in PFGE typing, indicating clonal transmission of E. coli among different animals. The detection of antimicrobial resistance and major antibiotic resistance genes and the plasmid transfer results showed that strains from different sources had high levels of resistance to commonly used clinical antibiotics and could be spread horizontally. Whole-genome sequencing discovered a novel ICE mobile element.

CONCLUSION

In summary, the antimicrobial resistance of E. coli in northeast China is a serious issue and there is a risk of antimicrobial resistance transmission. Meanwhile, a novel ICE mobile element appeared in the process of antimicrobial resistance formation.

Antimicrobial resistance genes in a golden jackal (Canis aureus L. 1758) from Central Italy

In recent years an increasing interest has been focused on the contribution of wildlife in ecology and evolution of the antimicrobial resistance (AMR). The aim of this study was to molecularly investigate the presence of antimicrobial resistance genes (ARGs) in organ samples from a golden jackal (Canis aureus) found dead in the Marche region (Central Italy). Samples from lung, liver, spleen, kidney, and intestine were investigated by PCRs targeting the following genes: tet(A), tet(B), tet(C), tet(D), tet(E), tet(G), tet(K), tet(L), tet(M), tet(O), tet(S), tet(P), tet(Q), tet(X), sul1, sul2, sul3, blaCTX-M, blaSHV, blaTEM, and mcr-1 to mcr-10. One or more ARGs were detected in all organs tested, except the spleen. Specifically, the lung and liver were positive for tet(M) and tet(P), the kidney for mcr-1 and the intestine for tet(A), tet(L), tet(M), tet(O), tet(P), sul3 and blaTEM-1. These results, according to the opportunistic foraging strategy of the jackal, confirm its potential role as a good bioindicator of AMR environmental contamination.

High prevalence of multidrug-resistant Escherichia coli in retail aquatic products in China and the first report of mcr-1-positive extended-spectrum β-lactamase-producing E. coli ST2705 and ST10 in fish

Contamination of food by multidrug-resistant (MDR) bacteria is a potential threat to consumers. Aquatic products are increasingly consumed due to their high value and rich nutrient. Nevertheless, the prevalence of multi-drug resistant (MDR) E. coli in retail aquatic products has not been systematically investigated in China. In this study, we conducted a national investigation on the prevalence of E. coli and MDR E. coli in retail aquatic products and the characteristics of the MDR E. coli isolates. A total of 849 samples consisting of 680 fish, 143 shrimp, and 26 shellfish were purchased from markets in 39 cities in China and investigated for the presence of E. coli. Overall, 340 (40.0 %) and 169 (19.9 %) samples were contaminated with E. coli and MDR E. coli, indicating poor hygiene conditions of retail aquatic products. A total of 190 MDR E. coli were isolated, which were recovered from 38.5 % shellfish, 20.1 % shrimp, and 19.0 % fish. Thirty-two ESBL-producing E. coli were identified from 3.5 % fish, 3.5 % shrimp, and 3.8 % shellfish. The MDR E. coli isolates showed a high prevalence of resistance to tetracycline (93.7 %), trimethoprim-sulfamethoxazole (78.9 %), ampicillin (78.4 %), chloramphenicol (72.1 %), nalidixic acid (73.2 %), cephalothin (65.3 %), and streptomycin (65.8 %). Resistances to kanamycin (42.1 %), gentamicin (37.9 %), ciprofloxacin (42.6 %), and norfloxacin (45.8 %) were also common. Further, 15.3 % and 8.4 % of the isolates were resistant to cefotaxime and ceftazidime, respectively. Four isolates were resistant to colistin. More than 85.0 % of the isolates were resistant to 5-15 antibiotics. Of the antibiotic resistance genes, TEM-1, tetA, strA/B, sul2, aadA, floR, and qnrS were the most prevalent, followed by sul1, aac(6')-Ib, oqxA/B, cmlA and aphA1. Six CTX-M-types were found, among which CTX-M-55 and CTX-M-14 were predominant. All 4 colistin-resistant isolates carried the mcr-1 gene, of which three were ESBL strains. WGS indicated that the mcr-1 gene was located on two types of plasmids (IncHI2 and IncX4). Conjugation experiments showed the mcr-1 gene could be transferred to E. coli C600. To our knowledge, this is the first report of mcr-1-positive ESBL E. coli (ST10 and ST2705) in retail aquatic products. The emergence of such strains poses a serious threat to consumers, with the potential to spread resistance genes to humans. Our results indicate that retail aquatic products are important reservoirs of MDR E. coli and facilitate the dissemination of the resistance genes. Continuous surveillance and interventions of restricting antibiotic use in aquatic environments should also be applied to reduce the prevalence of MDR bacteria.

Detection and genetic characterization of blaESBL-carrying plasmids of cloacal Escherichia coli isolates from white stork nestlings (Ciconia ciconia) in Spain

OBJECTIVES

This study aimed to characterize Escherichia coli isolates from cloacal samples of white stork nestlings, with a special focus on extended-spectrum β-lactamases (ESBLs)-producing E. coli isolates and their plasmid content.

METHODS

Cloacal samples of 88 animals were seeded on MacConkey-agar and chromogenic-ESBL plates to recover E. coli and ESBL-producing E. coli. Antimicrobial susceptibility was screened using the disc diffusion method, and the genotypic characterization was performed by polymerase chain reaction (PCR) and subsequent sequencing. S1 nuclease Pulsed-Field-Gel-Electrophoresis (PFGE), Southern blotting, and conjugation essays were performed on ESBL-producing E. coli, as well as whole-genome sequencing by short- and long-reads. The four blaESBL-carrying plasmids were completely sequenced.

RESULTS

A total of 113 non-ESBL-producing E. coli isolates were collected on antibiotic-free MacConkey-agar, of which 27 (23.9%) showed a multidrug-resistance (MDR) phenotype, mainly associated with β-lactam-phenicol-sulfonamide resistance (blaTEM/cmlA/floR/sul1/sul2/sul3). Moreover, four white stork nestlings carried ESBL-producing E. coli (4.5%) with the following characteristics: blaSHV-12/ST38-D, blaSHV-12/ST58-B1, blaCTX-M-1/ST162-B1, and blaCTX-M-32/ST155-B1. Whole-genome sequencing followed by Southern blot hybridizations on S1-PFGE gels in ESBL-positive isolates proved that the blaCTX-M-1 gene and one of the blaSHV-12 genes were carried by IncI1/pST3 plasmids, while the second blaSHV-12 gene and the blaCTX-M-32 gene were located on IncF plasmids. The two blaSHV-12 genes and the two blaCTX-M genes had similar but non-identical close genetic environments, as all four genes were flanked by a variety of insertion sequences.

CONCLUSION

The role played by several genetic platforms in the mobility of ESBL genes allows for interchangeability on a remarkably small scale (gene-plasmid-clones), which may support the spread of ESBL genes.

Biofilm-forming antimicrobial-resistant pathogenic Escherichia coli: A one health challenge in Northeast India

This study aimed to investigate the prevalence of Shiga toxin-producing Escherichia coli (STEC), Enteropathogenic E. coli (EPEC), and Enterotoxigenic E. coli (ETEC) in common food animals (cattle, goats, and pigs) reared by tribal communities and smallholder farmers in Northeast India. The isolates were characterized for the presence of virulence genes, extended-spectrum beta-lactamases (ESBL) production, antimicrobial resistance, and biofilm production, and the results were statistically interpreted. In pathotyping 141 E. coli isolates, 10 (7.09%, 95% CI: 3.45%-12.66%) were identified as STEC, 2 (1.42%, 95% CI: 0.17%-5.03%) as atypical-EPEC, and 1 (0.71%, 95% CI: 0.02%-3.89%) as typical-EPEC. None of the isolates were classified as ETEC. Additionally, using the phenotypic combination disc method (ceftazidime with and without clavulanic acid), six isolates (46.1%, 95% CI: 19.22%-74.87%) were determined to be ESBL producers. Among the STEC/EPEC strains, eleven (84.6%, 95% CI: 54.55%-98.08%) and one (7.7%, 95% CI: 0.19%-36.03%) strains were capable of producing strong or moderate biofilms, respectively. PFGE analysis revealed indistinguishable patterns for certain isolates, suggesting clonal relationships. These findings highlight the potential role of food animals reared by tribal communities and smallholder farmers as reservoirs of virulent biofilm-forming E. coli pathotypes, with implications for food contamination and zoonotic infections. Therefore, monitoring these pathogens in food animals is crucial for optimizing public health through one health strategy.

Comparative genetic characterisation of third-generation cephalosporin-resistant Escherichia coli isolated from integrated and conventional pig farm in Korea

OBJECTIVES

Pig-farming systems consist of integrated or conventional farms, and many antimicrobials are used to treat bacterial infections. The objective of this study was to compare characteristics of third-generation cephalosporin resistance and extended-spectrum β-lactamase (ESBL)/pAmpC β-lactamase-producing Escherichia coli between integrated and conventional farms.

METHODS

Third-generation cephalosporin-resistant E. coli was collected from integrated and conventional pig farms from 2021 to 2022. Polymerase chain reaction and DNA sequencing were performed for the detection of β-lactamase-encoding genes, molecular analysis, and identification of genetic relationships. To determine the transferability of β-lactamase genes, conjugation assays were conducted.

RESULTS

Antimicrobial resistance rates were higher in conventional farms than in integrated farms; ESBL- and pAmpC-lactamase-producing E. coli rates were higher in conventional farms (9.8%) than in integrated farms (3.4%). Fifty-two (6.5%) isolates produced ESBL/pAmpC β-lactamase genes. Isolates from integrated farms harboured CTX-15 (3 isolates), CTX-55 (9 isolates), CTX-229 (1 isolate), or CMY-2 (1 isolate) genes; isolates from conventional farms harboured CTX-1 (1 isolate), CTX-14 (6 isolates), CTX-15 (2 isolates), CTX-27 (3 isolates), CTX-55 (14 isolates), CTX-229 (1 isolate), and CMY-2 (11 isolates) genes. Of the 52 ESBL/pAmpC β-lactamase-producing E. coli isolates, class 1 integrons with 11 different gene cassette arrangements were detected in 39 (75.0%) isolates, and class 2 integrons were detected in 3 isolates. The most common sequence type in both integrated and conventional farms was ST5229, followed by ST101, and then ST10.

CONCLUSION

Third-generation cephalosporin-resistant patterns and molecular characteristics differed between integrated and conventional farms. Our findings suggest that continuous monitoring of third-generation cephalosporin resistance on pig farms is necessary to prevent the dissemination of resistant isolates.

Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene

Trimethoprim (TMP) is a low-cost, widely prescribed antibiotic. Its effectiveness is increasingly challenged by the spread of genes coding for TMP-resistant dihydrofolate reductases: dfrA, and the lesser-known, evolutionarily unrelated dfrB. Despite recent reports of novel variants conferring high level TMP resistance (dfrB10 to dfrB21), the prevalence of dfrB is still unknown due to underreporting, heterogeneity of the analyzed genetic material in terms of isolation sources, and limited bioinformatic processing. In this study, we explored a coherent set of shotgun metagenomic sequences to quantitatively estimate the abundance of dfrB gene variants in aquatic environments. Specifically, we scanned sequences originating from influents and effluents of municipal sewage treatment plants as well as river-borne microbiomes. Our analyses reveal an increased prevalence of dfrB1, dfrB2, dfrB3, dfrB4, dfrB5, and dfrB7 in wastewater microbiomes as compared to freshwater. These gene variants were frequently found in genomic neighborship with other resistance genes, transposable elements, and integrons, indicating their mobility. By contrast, the relative abundances of the more recently discovered variants dfrB9, dfrB10, and dfrB13 were significantly higher in freshwater than in wastewater microbiomes. Moreover, their direct neighborship with other resistance genes or markers of mobile genetic elements was significantly less likely. Our findings suggest that natural freshwater communities form a major reservoir of the recently discovered dfrB gene variants. Their proliferation and mobilization in response to the exposure of freshwater communities to selective TMP concentrations may promote the prevalence of high-level TMP resistance and thus limit the future effectiveness of antimicrobial therapies.

Evaluation of the Ability to Form Biofilms in KPC-Producing and ESBL-Producing Klebsiella pneumoniae Isolated from Clinical Samples

The appearance of Klebsiella pneumoniae strains producing extended-spectrum β-lactamase (ESBL), and carbapenemase (KPC) has turned into a significant public health issue. ESBL- and KPC-producing K. pneumoniae's ability to form biofilms is a significant concern as it can promote the spread of antibiotic resistance and prolong infections in healthcare facilities. A total of 45 K. pneumoniae strains were isolated from human infections. Antibiograms were performed for 17 antibiotics, ESBL production was tested by Etest ESBL PM/PML, a rapid test was used to detect KPC carbapenemases, and resistance genes were detected by PCR. Biofilm production was detected by the microtiter plate method. A total of 73% of multidrug resistance was found, with the highest resistance rates to ampicillin, trimethoprim-sulfamethoxazole, cefotaxime, amoxicillin-clavulanic acid, and aztreonam. Simultaneously, the most effective antibiotics were tetracycline and amikacin. bla_CTX-M, bla_TEM, bla_SHV, aac(3)-II, aadA1, tetA, cmlA, catA, gyrA, gyrB, parC, sul1, sul2, sul3, bla_KPC, bla_OXA, and bla_PER genes were detected. Biofilm production showed that 80% of K. pneumoniae strains were biofilm producers. Most ESBL- and KPC-producing isolates were weak biofilm producers (40.0% and 60.0%, respectively). There was no correlation between the ability to form stronger biofilms and the presence of ESBL and KPC enzymes in K. pneumoniae isolates.

First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes

The human gut microbiome plays a vital role in health and disease. In particular, the first days of life provide a unique window of opportunity for development and establishment of microbial community. Currently, stool samples are known to be the most widely used sampling approach for studying the gut microbiome. However, complicated sample acquisition at certain time points, challenges in transportation, and patient discomfort underline the need for development of alternative sampling approaches. One of the alternatives is rectal swabs, shown to be a reliable proxy for gut microbiome analysis when obtained from adults. Here, we compare the usability of rectal swabs and meconium paired samples collected from infants on the first days of life. Our results indicate that the two sampling approaches display significantly distinct patterns in microbial composition and alpha and beta diversity as well as detection of resistance genes. Moreover, the dissimilarity between the two collection methods was greater than the interindividual variation. Therefore, we conclude that rectal swabs are not a reliable proxy compared to stool samples for gut microbiome analysis when collected on the first days of a newborn's life. IMPORTANCE Currently, there are numerous suggestions on how to ease the notoriously complex and error-prone methodological setups to study the gut microbiota of newborns during the first days of life. Especially, meconium samples are regularly failing to yield meaningful data output and therefore have been suggested to be replaced by rectal swabs as done in adults as well. We find this development toward a simplified method to be producing dramatically erroneous results, skewing data interpretation away from the real aspects to be considered for neonatal health during the first days of life. We have put together our knowledge on this critical aspect with careful consideration and identified the failure of rectal swabs to be a replacement for sampling of meconium in term-born newborns.

Resistance and virulence gene analysis and molecular typing of Escherichia coli from duck farms in Zhanjiang, China

Introduction

The widespread use of antibiotics in animal agriculture has increased the resistance of Escherichia coli, and pathogenic E. coli often harbor complex virulence factors. Antimicrobial resistance in pathogenic bacteria can cause public health problems. Correlation analyses of the resistance, virulence, and serotype data from the pathogenic bacteria found on farms and in the surrounding environment can thus provide extremely valuable data to help improve public health management.

Methods

In this investigation, we have assessed the drug resistance and virulence genes as well as the molecular typing characteristics of 30 E. coli strains isolated from duck farms in the Zhanjiang area of China. Polymerase chain reaction was used to detect the drug resistance and virulence genes as well as serotypes, and whole-genome sequencing was used to analyze the multilocus sequence typing.

Results

The detection rates for the oqxA resistance gene and fimC virulence gene were highest (93.3%, respectively). There were no correlations between the drug resistance and virulence gene numbers in the same strain. The epidemic serotype was O81 (5/24), ST3856 was an epidemic sequence type, and strains I-9 and III-6 carried 11 virulence genes. The E. coli strains from the duck farms in the Zhanjiang area were thus found to have a broad drug resistance spectrum, various virulence genes, complex serotypes, and certain pathogenicity and genetic relationship.

Discussion

Monitoring the spread of pathogenic bacteria and the provision of guidance regarding the use of antibiotics in the livestock and poultry industries will be required in the future in the Zhanjiang area.

Cost-effective one-spot hydrothermal synthesis of graphene oxide nanoparticles for wastewater remediation: AI-enhanced approach for transition metal oxides

This investigation presents a cost-efficient hydrothermal synthesis technique for producing graphene oxide nanoparticles (GO-NPs) that exhibit promising potential in wastewater treatment. The synthesis process involves a facile and expandable hydrothermal reactor that can be regulated using an AI-empowered methodology. The generated GO-NPs were characterised using X-ray diffraction (XRD), Fourier-transform infrared (FTIR) spectroscopy, Raman spectroscopy, and transmission electron microscopy (TEM), confirming their successful synthesis and high quality. The high degree of crystallinity observed in the GO-NPs can be attributed to the favourable reaction conditions facilitated by the hydrothermal synthesis. The TEM analysis showed that the GO-NPs had a homogeneous dispersion pattern and a consistent size distribution of approximately 10 nm. Carboxylation was employed to functionalize the GO-NPs, enhancing their reactivity towards diverse contaminants present in wastewater. The remediation potential of the GO-NPs for transition metal oxides, which are frequently found in wastewater, was assessed. The GO-NPs exhibited notable efficacy in remediating the transition metal oxides that were subjected to testing. The heightened efficacy of remediation can be attributed to the substantial surface area and elevated reactivity of the GO-NPs, in addition to their functionalization using carboxylic groups. The cost-effective and efficient synthesis method, coupled with the high remediation potential of the GO-NPs, makes them a highly promising contender for employment in wastewater remediation applications. The use of AI in regulating the hydrothermal synthesis procedure enables accurate manipulation of the reaction parameters, thereby augmenting the quality and uniformity of the resultant GO-NPs. The proposed method exhibits scalability potential for large-scale production of GO-NPs, presenting a viable remedy for the challenges associated with wastewater remediation.

Contribution of efflux and mutations in fluoroquinolone susceptibility in MDR enterobacterial isolates: a quantitative and molecular study

OBJECTIVES

The emergence of MDR strains is a public health problem in the management of associated infections. Several resistance mechanisms are present, and antibiotic efflux is often found at the same time as enzyme resistance and/or target mutations. However, in the laboratory routinely, only the latter two are identified and the prevalence of antibiotic expulsion is underestimated, causing a misinterpretation of the bacterial resistance phenotype. The development of a diagnostic system to quantify the efflux routinely would thus improve the management of patients.

METHODS

A quantitative technique based on detection of clinically used fluoroquinolones was investigated in Enterobacteriaceae clinical strains with a high or basal efflux activity. The detail of efflux involvement was studied from MIC determination and antibiotic accumulation inside bacteria. WGS was carried out on selected strains to determine the genetic background associated with efflux expression.

RESULTS

Only 1 Klebsiella pneumoniae isolate exhibited a lack of efflux whereas 13 isolates had a basal efflux and 8 presented efflux pump overexpression. The antibiotic accumulation evidenced the efficacy of the efflux mechanism in strains, and the contribution of dynamic expulsion versus target mutations in fluoroquinolone susceptibility.

CONCLUSIONS

We confirmed that phenylalanine arginine β-naphthylamide is not a reliable marker of efflux due to the affinity of the AcrB efflux pump for different substrates. We have developed an accumulation test that can be used efficiently on clinical isolates collected by the biological laboratory. The experimental conditions and protocols ensure a robust assay that with improvements in practice, expertise and equipment could be transferred to the hospital laboratory to diagnose the contribution of efflux in Gram-negative bacteria.

Comparative Analysis between Salmonella enterica Isolated from Imported and Chinese Native Chicken Breeds

Salmonella enterica is considered a significant threat to the global poultry industry and public health. In recent decades, antimicrobial resistance in Salmonella enterica has attracted increasing concern throughout the world. However, limited information is available on Salmonella enterica among different breeds of breeder chickens. Thus, this study aimed to compare the prevalence, serotype distribution, emergence of extended-spectrum beta-lactamases (ESBLs), antimicrobial resistance, and genetic resistance mechanisms in Salmonella enterica among different breeds of breeder chickens. A total of 693 samples (dead embryos, cloacal swabs, water, feed, environmental swabs, and meconium of newly hatched chicks) were selected and cultured for Salmonella from four breeder chicken farms in Shandong province, China, representing one imported and three native breeds, and the isolates were further serotyped. Of the Salmonella isolates, susceptibility to 11 antimicrobials of 5 classes, ESBL screening, and the presence of 21 antimicrobial resistance genes were determined in the present study. Overall, 94 (13.6%) isolates were recovered, which were divided into 3 serotypes (Salmonella Pullorum (n = 36), Salmonella Thompson (n = 32), and Salmonella Enteritidis (n = 26)). The results showed that the prevalence of Salmonella enterica isolates from the imported breeds was higher compared with the three domestic breeds. Eight of the ninety-four isolates were ESBL-positive strains, which were recovered from a domestic breed chicken farm. These eight ESBL-producing isolates were serotyped to Pullorum. Surprisingly, Salmonella Enteritidis (S. enteritidis) and S. pullorum were simultaneously isolated from a single dead embryo observed among one native breed. Meanwhile, among the Salmonella isolates, 53.2% (50/94) were multidrug-resistant strains, and 44.7% (42/94) of the isolates presented resistance to at least five antibiotics. Nearly all of the isolates (97.9%, 92/94) were resistant to at least one antimicrobial; one isolate of S. Thompson was resistant to seven antimicrobial agents belonging to four different classes. The carriage rate of three resistance genes (tetA, tetB, and sul1) among isolates from the imported breeds (87%, 70%, and 65.2%) was higher than that in those from domestic breeds (35.2%, 36.6, and 14.1%). To our knowledge, this is the first report of ESBLs-producing Salmonella isolated from a Chinese native breed of breeder chickens. Our results also highlight that a high prevalence of multidrug-resistant Salmonella enterica contamination is widespread among different breeds of breeder chickens, which is a major risk of food-borne diseases and public health.

High Biofilm-Forming Ability and Clonal Dissemination among Colistin-Resistant Escherichia coli Isolates Recovered from Cows with Mastitis, Diarrheic Calves, and Chickens with Colibacillosis in Tunisia

BACKGROUND

Escherichia coli (E. coli) is one of the main etiological agents responsible for bovine mastitis (BM), neonatal calf diarrhea (NCD), and avian colibacillosis (AC). This study aimed to assess resistance and virulence genes content, biofilm-forming ability, phylogenetic groups, and genetic relatedness in E. coli isolates recovered from clinical cases of BM, NCD, and AC.

MATERIALS/METHODS

A total of 120 samples including samples of milk (n = 70) and feces (n = 50) from cows with BM and calves with NCD, respectively, were collected from different farms in Northern Tunisia. Bacterial isolation and identification were performed. Then, E. coli isolates were examined by disk diffusion and broth microdilution method for their antimicrobial susceptibility and biofilm-forming ability. PCR was used to detect antimicrobial resistance genes (ARGs), virulence genes (VGs), phylogenetic groups, and Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) for their clonal relationship.

RESULTS

Among the 120 samples, 67 E. coli isolates (25 from BM, 22 from AC, and 20 from NCD) were collected. Overall, 83.6% of isolates were multidrug resistant. Thirty-six (53.73%) isolates were phenotypically colistin-resistant (CREC), 28.3% (19/67) were ESBL producers (ESBL-EC), and forty-nine (73.1%) formed biofilm. The bla_TEM gene was found in 73.7% (14/19) of isolates from the three diseases, whilst the bla_CTXM-g-1 gene was detected in 47.3% (9/19) of isolates, all from AC. The most common VG was the fimA gene (26/36, 72.2%), followed by aer (12/36, 33.3%), cnf1 (6/36, 16.6%), papC (4/36, 11.1%), and stx1 and stx2 genes (2/36; 5.5% for each). Phylogenetic analysis showed that isolates belonged to three groups: A (20/36; 55.5%), B2 (7/36; 19.4%), and D (6/36; 16.6%). Molecular typing by ERIC-PCR showed high genetic diversity of CREC and ESBL E. coli isolates from the three animal diseases and gave evidence of their clonal dissemination within farms in Tunisia.

CONCLUSION

The present study sheds new light on the biofilm-forming ability and clonality within CREC and ESBL-EC isolated from three different animal diseases in Tunisian farm animals.

Comparative genetic characterization of CMY-2-type beta-lactamase producing pathogenic Escherichia coli isolated from humans and pigs suffering from diarrhea in Korea

BACKGROUND

Pathogenic Escherichia coli are an important cause of bacterial infections in both humans and pigs and many of antimicrobials are used for the treatment of E. coli infection. The objective of this study was to investigate the characteristics and relationship between humans and pigs regarding third-generation cephalosporin resistance and CMY-2-producing E. coli in Korea.

RESULTS

All 103 third-generation cephalosporin-resistant E. coli isolates showed multidrug resistance. Also, except for β-lactam/β-lactamase inhibitor combinations, all antimicrobials resistant rates were higher in pigs than in humans. A total of 36 isolates (humans: five isolates; pigs: 31 isolates) were positive for the CMY-2-encoding genes and thirty-two (88.9%) isolates detected class 1 integrons with 10 different gene cassette arrangements, and only 1 isolate detected a class 2 integron. The most common virulence genes in pigs were LT (71.0%), F18 (51.6%), and STb (51.6%), while stx2 (80.0%) was the most frequently detected gene in humans. Stx2 gene was also detected in pigs (6.5%). Interestingly, 36 CMY-2-producing E. coli isolates showed a high diversity of sequence types (ST), and ST88 was present in E. coli from both pigs (11 isolates) and humans (one isolate).

CONCLUSION

Our findings suggest that a critical need for comprehensive surveillance of third-generation cephalosporin resistance is necessary to preserve the usefulness of third-generation cephalosporins in both humans and pigs.

First Report of IMI-2-Producing Enterobacter bugandensis and CTX-M-55-Producing Escherichia coli isolated from Healthy Volunteers in Tunisia

The aim of this study was to characterize the prevalence of fecal carriage of extended-spectrum beta-lactamases and carbapenemase-producing Gram-negative bacteria among healthy humans in Tunisia. Fifty-one rectal swabs of healthy volunteers were plated on MacConkey agar plates supplemented with cefotaxime or imipenem. The occurrences of resistance genes, integrons, and phylogroup typing were investigated using PCR and sequencing. The genetic relatedness of isolates was determined by pulsed-field-gel-electrophoresis (PFGE) and multilocus-sequence-typing (MLST). Whole-genome-sequencing (WGS) was performed for the carbapenem-resistant isolate. Sixteen ESBL-producing Escherichia coli isolates and one carbapenem-resistant Enterobacter bugandensis were detected out of the fifty-one fecal samples. The ESBL-producing E. coli strains contained genes encoding CTX-M-15 (n = 9), CTX-M-1 (n = 3), CTX-M-27 (n = 3), and CTX-M-55 (n = 1). Three CTX-M-1-producers were of lineages ST131, ST7366, and ST1158; two CTX-M-15-producers belonged to lineage ST925 and ST5100; one CTX-M-27-producer belonged to ST2887, and one CTX-M-15-producer belonged to ST744. Six isolates contained class 1 integrons with the following four gene cassette arrangements: dfrA5 (two isolates), dfrA12-orf-aadA2 (two isolates), dfrA17-aadA5 (one isolate), and aadA1 (one isolate). E. bugandensis belonged to ST1095, produced IMI-2 carbapenemase, and contained qnrE1 and fosA genes. A genome-sequence analysis of the E. bugandensis strain revealed new mutations in the bla_ACT and qnr genes. Our results reveal an alarming rate of ESBL-E. coli in healthy humans in Tunisia and the first description of IMI-2 in E. bugandensis.

Multidrug-resistant extended spectrum β-lactamase (ESBL)-producing Escherichia coli from farm produce and agricultural environments in Edo State, Nigeria

Antimicrobial resistance (AMR) is a major public health concern, especially the extended-spectrum β-lactamase-producing (ESBL) Escherichia coli bacteria are emerging as a global human health hazard. This study characterized extended-spectrum β-lactamase Escherichia coli (ESBL-E. coli) isolates from farm sources and open markets in Edo State, Nigeria. A total of 254 samples were obtained in Edo State and included representatives from agricultural farms (soil, manure, irrigation water) and vegetables from open markets, which included ready-to-eat (RTE) salads and vegetables which could potentially be consumed uncooked. Samples were culturally tested for the ESBL phenotype using ESBL selective media, and isolates were further identified and characterized via polymerase chain reaction (PCR) for β-lactamase and other antibiotic resistance determinants. ESBL E. coli strains isolated from agricultural farms included 68% (17/25) from the soil, 84% (21/25) from manure and 28% (7/25) from irrigation water and 24.4% (19/78) from vegetables. ESBL E. coli were also isolated from RTE salads at 20% (12/60) and vegetables obtained from vendors and open markets at 36.6% (15/41). A total of 64 E. coli isolates were identified using PCR. Upon further characterization, 85.9% (55/64) of the isolates were resistant to ≥ 3 and ≤ 7 antimicrobial classes, which allows for characterizing these as being multidrug-resistant. The MDR isolates from this study harboured ≥1 and ≤5 AMR determinants. The MDR isolates also harboured ≥1 and ≤3 beta-lactamase genes. Findings from this study showed that fresh vegetables and salads could be contaminated with ESBL-E. coli, particularly fresh produce from farms that use untreated water for irrigation. Appropriate measures, including improving irrigation water quality and agricultural practices, need to be implemented, and global regulatory guiding principles are crucial to ensure public health and consumer safety.

A comparative study of different docking methodologies to assess the protein-ligand interaction for the E. coli MurB enzyme

We have investigated the active site of E. coli MurB using the Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The docking of three novel series of 4-thiazolidinone derivatives has been performed using two methods: rigid docking and flexible docking (Induced Fit Docking: IFD). The results have been compared to understand the conformational aspects of the enzyme. The docking results from rigid docking show that the ligands with highly negative ΔG_bind have poor docking scores. In addition, the value of the regression coefficient (R) obtained on correlating the ΔG_bind and the experimental pMIC values is insignificant. On keeping the protein flexible, there is a remarkable improvement in both the docking score and ΔG_bind, along with a good value of R (0.64). Two important residues, Tyr254 and Try190 are found to be highly displaced during the flexible docking and hence their role in effective ligand binding has been confirmed. Thus, comparing the two methodologies, IFD has emerged as the more appropriate one for studying the E. coli MurB enzyme. To further substantiate the findings, MD studies over a time period of 20 ns have been performed on the IFD-LIII j and Rigid/XP-LIII j complexes and the results shows the former complex to be more stable, with lower average RMSD and higher average ΔG_bind.Communicated by Ramaswamy H. Sarma.

Examining the impact of zinc on horizontal gene transfer in Enterobacterales

Antimicrobial resistance is one of the main international health concerns for humans, animals, and the environment, and substantial efforts have focused on reducing its development and spread. While there is evidence for correlations between antimicrobial usage and antimicrobial resistance development, specific information on the effect of heavy metal/antimicrobial usage on bacterial conjugation is more limited. The aim of this study was to investigate the effects of zinc and antimicrobials in different concentrations on horizontal gene transfer of an ampicillin resistance gene, using a multi-drug resistant Escherichia coli donor strain and three different Salmonella enterica serovars as recipient strains. Differences in conjugation frequencies for the different Salmonella recipients were observed, independent of the presence of zinc or the antimicrobials. Selective pressure on the recipient strains, in the form of ampicillin, resulted in a decrease in conjugation frequencies, while, the presence of rifampicin resulted in increases. Zinc exposure affected conjugation frequencies of only one of the three recipient strains, thus the effect of zinc on conjugation frequencies seemed to be concentration and strain dependent. Furthermore, differences in growth rates due to plasmid carriage were observed for one of the Salmonella strains.

Antimicrobial Resistance Pattern of Escherichia coli Isolates from Small Scale Dairy Cattle in Dar es Salaam, Tanzania

Simple Summary

Dearth of information on antimicrobial resistance (AMR) in small-scale dairy cattle in Dar es Salaam, the commercial city of Tanzania, prompted us to conduct this study. The objective was to determine the different levels of resistance phenotypical patterns among Escherichia coli (E. coli) isolates from rectal swabs of apparently healthy cattle. Antimicrobial resistance occurs when microorganisms develop the ability to tolerate antimicrobial concentrations to which they were initially susceptible. It is a phenomenon of global concern, which is on the rise due to antimicrobial use in food-producing animals. In dairy farms, cattle carry high levels of AMR Escherichia coli (E. coli), and may act as a potential reservoir. The study revealed that resistance to ampicillin, cefotaxime, tetracycline and trimethoprim/sulfamethoxazole was the most frequent. Resistance to nalidixic acid, ciprofloxacin, chloramphenicol, and gentamycin was also observed among the E. coli isolates, but with lower percentages. E. coli resistant to third generation cephalosporins was also detected. The results of the current study give an insight into the status of antimicrobial resistance and multidrug resistance in small-scale dairy cattle in Dar es Salaam, Tanzania. The findings call for further research, prudent antimicrobial use, and surveillance initiatives.

Abstract

In Tanzania, information on antimicrobial resistance in small-scale dairy cattle is scarce. This cross-sectional study was conducted to determine the different levels and pattern of antimicrobial resistance (AMR), in 121 Escherichia coli isolated from rectal swab of 201 apparently healthy small-scale dairy cattle in Dar es Salaam, Tanzania. Isolation and identification of E. coli were carried out using enrichment media, selective media, and biochemical tests. Antimicrobial susceptibility testing was carried out using the Kirby–Bauer disk diffusion method on Mueller-Hinton agar (Merck), according to the recommendations of Clinical and Laboratory Standards Institute (CLSI). Resistance was tested against ampicillin, gentamicin, chloramphenicol, trimethoprim-sulfamethoxazole, tetracycline, nalidixic acid, ciprofloxacin and cefotaxime. Resistance to almost all antimicrobial agents was observed. The agents to which resistance was demonstrated most frequently were ampicillin (96.7%), cefotaxime (95.0%), tetracycline (50.4%), trimethoprim-sulfamethoxazole (42.1%) and nalidixic acid (33.1%). In this case, 20 extended-spectrum beta-lactamases (ESBLs) producing E. coli were identified. 74.4% (90/121) of the isolates were Multidrug resistant (MDR), ranging from a combination of three to 8 different classes. The most frequently observed phenotypes were AMP-SXT-CTX with a prevalence of 12.4%, followed by the combination AMP-CTX with 10.7% and TE-AMP-CTX and NA + TE + AMP + CTX with 8.3% each. The high prevalence and wide range of AMR calls for prudent antimicrobial use.

Multidrug resistant Escherichia coli from fresh produce sold by street vendors in South African informal settlements

The aim of this study was to assess the prevalence of commensal and pathogenic Escherichia coli on informally sold fresh produce in South Africa, who harbour and express antimicrobial resistance genes and therefore pose indirect risks to public health. The majority (85.71%) of E. coli isolates from spinach, apples, carrots, cabbage and tomatoes, were multidrug resistant (MDR). Resistance to Aminoglycoside (94.81%), Cephalosporin (93.51%), Penicillin (93.51%) and Chloramphenicol (87.01%) antibiotic classes were most prevalent. Antibiotic resistance genes detected included bla_TEM (89.29%), tetA (82.14%), tetB (53.57%), tetL (46.43%), sulI (41.07%), sulII (51.79%), aadA1a (58.93%) and strAB (51.79%). A single isolate was found to harbour eae virulence factor. Moreover, E. coli isolates were grouped into the intra-intestinal infectious phylogenetic group E (28.57%), the rare group C (26.79%), the generalist group B1 (21.43%) and the human commensal group A (16.07%). Presence of MDR E. coli represents a transmission route and significant human health risk.

Companion Animals as Potential Reservoirs of Antibiotic Resistant Diarrheagenic Escherichia coli in Shandong, China

Antibiotic resistance genes of Escherichia coli (E. coli) from companion animals were still poorly understood. Here, we investigated the extended-spectrum β-lactamases (ESBLs) resistance genes of E. coli from companion animals in Shandong, China. A total of 79 isolates (80.6%) were recovered from 98 healthy or diarrheal companion animals in 2021, among which ESBLs-producing isolates accounted for 43.0% (34/79), and more than half of ESBL E. coli (ESBL-EC) strains (n = 19) were isolated from healthy companion animals. Diarrheagenic E. coli isolates (45.6%, n = 36) were represented by enterotoxigenic (ETEC) (32.9%), enteropathogenic (EPEC) (10.1%) and enteroinvasive (EIEC) (2.6%), 20 isolates of which were from healthy pets. Among tested antibiotics, resistance to tetracycline (64.6%) was the most commonly observed, followed by doxycycline (59.5%) and ampicillin (53.2%). Notably, all isolates were susceptible to meropenem. The multidrug-resistant (MDR) rate was 49.4%, 20 isolates of which were ESBLs producers; moreover, 23.4%, 16.4% of ESBL-EC strains were resistant to 5 or more, 7 or more antibiotics, respectively. Among the 5 β-lactamase resistance genes, the most frequent gene was bla_CTX-M (60.76%), followed by bla_SHV (40.51%). The plasmid-mediated quinolone resistance (PMQR) gene aac(6')-Ib-cr was detected in 35 isolates. Additionally, ESBL-associated genes (i.e., bla_CTX-M, bla_SHV) were found in 76.5% ESBL-EC strains, with six isolates carrying bla_CTX-M and bla_SHV. The marker gene of high-pathogenicity island gene irp2 (encoding iron capture systems) was the most frequency virulence gene. Our results showed that ESBL-EC were widespread in healthy or diarrhea companion animals, especially healthy pets, which may be a potential reservoir of antibiotic resistance, therefore, enhancing a risk to public and animal health.

Risk of sharing resistant bacteria and/or resistance elements between dogs and their owners

Background

The indiscriminate use and the similarity of prescribed antibiotics especially beta-lactams in human and small animal medicine, along with the close communication between pets and humans, increases the risk of the transfer of antibiotic-resistant bacteria and/or resistance elements especially integrons, between them. Therefore, we aimed to compare the frequencies of extended spectrum beta-lactamase (ESBL)-producing strains, major ESBL genes, classes 1 and 2 integrons, and antibiotic resistance patterns of fecal Escherichia coli (E. coli) isolates from dogs and their owners.

Methods

The present study was conducted on 144 commensal E. coli isolates from the feces of 28 healthy dog-owner pairs and 16 healthy humans who did not own pets. Phenotypic confirmatory test was used to identify the frequencies of ESBL-producing E. coli. Frequencies of bla_CTX-M, bla_SHV, and bla_TEM genes, and also classes 1 and 2 integrons were determined by polymerase chain reaction. Resistance against 16 conventional antibiotics was determined by disk diffusion technique.

Results

ESBL-production status was similar between the E. coli isolates of 71.4% of dog-owner pairs. The E. coli isolates of 75, 60.7, and 85.7% of dog-owner pairs were similar in terms of the presence or absence of bla_CTX-M, bla_TEM, and bla_SHV genes, respectively. The presence or absence of class 1 and class 2 integrons was the same in E. coli isolates of 57.1% of dog-owner pairs. Prevalence of resistance to chloramphenicol and tetracycline was significantly higher in E. coli isolates of dogs than owners, but for other 10 (83.3%) tested antibiotics, no statistically significant difference was found in prevalence of antibiotic resistance between dogs and owners isolates. Furthermore, the antibiotic-resistance profile was the same in the E. coli isolates of 14.3% of dog-owner pairs.

Conclusions

The results of current research highlight the seriousness of the drug-resistance problem and the need to prevent further increases and spread of antibiotic-resistance to reduce treatment failure. Moreover, relatively similar characteristics of the E. coli isolates of dogs and their owners can show the risk of sharing resistant bacteria and/or resistance elements between them.

Public health implications of plasmid-mediated quinolone and aminoglycoside resistance genes in Escherichia coli inhabiting a major anthropogenic river of India

Presence of antimicrobial resistance (AMR) genes in Escherichia coli inhabiting anthropogenic rivers is an important public health concern because plasmid-mediated AMR genes can easily spread to other pathogens by horizontal gene transfer. Besides β -lactams, quinolones and aminoglycosides are the major antibiotics against E. coli. In the present study, we have investigated the presence of plasmid-mediated quinolone resistance (PMQR) and aminoglycoside resistance genes in E. coli isolated from a major river of northern India. Our results revealed that majority of the strains were phenotypically susceptible for fluoroquinolones and some aminoglycosides like amikacin, netilmicin, tobramycin and gentamicin. However, 16.39% of the strains were resistant for streptomycin, 8.19% for kanamycin and 3.30% for gentamicin. Of the various PMQR genes investigated, only qnrS1 was present in 24.59% of the strains along with ISEcl2 . Aminoglycoside-resistance genes like strA-strB were found to be present in 16.39%, aphA1 in 8.19% and aacC 2 in only 3.30% of the strains. Though, no co-relation was observed between phenotypic resistance for fluorquinolones and presence of PMQR genes, phenotypic resistance for streptomycin, kanamycin and gentamicin exactly co-related with the presence of the genes strA-strB , aphA1 and aacC2 , respectively. Moreover, all the AMR genes discerned in aquatic E. coli were found to be situated on conjugative plasmids and, thus easily transferrable. Our study accentuates the importance of routine surveillance of urban rivers to curtail the spread of AMR genes in aquatic pathogens.