Extensive Drug-Resistant Salmonella enterica Isolated From Poultry and Humans: Prevalence and Molecular Determinants Behind the Co-resistance to Ciprofloxacin and Tigecycline

Adaptive evolution of carbapenem-resistant hypervirulent Klebsiella pneumoniae in the urinary tract of a single patient

The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) is a growing concern due to its high mortality and limited treatment options. Although hypermucoviscosity is crucial for CR-hvKp infection, the role of changes in bacterial mucoviscosity in the host colonization and persistence of CR-hvKp is not clearly defined. Herein, we observed a phenotypic switch of CR-hvKp from a hypermucoviscous to a hypomucoviscous state in a patient with scrotal abscess and urinary tract infection (UTI). This switch was attributed to decreased expression of rmpADC, the regulator of mucoid phenotype, caused by deletion of the upstream insertion sequence ISKpn26. Postswitching, the hypomucoid variant showed a 9.0-fold decrease in mice sepsis mortality, a >170.0-fold reduction in the ability to evade macrophage phagocytosis in vitro, and an 11.2- to 40.9-fold drop in growth rate in normal mouse serum. Conversely, it exhibited an increased residence time in the mouse urinary tract (21 vs. 6 d), as well as a 216.4-fold boost in adhesion to bladder epithelial cells and a 48.7% enhancement in biofilm production. Notably, the CR-hvKp mucoid switch was reproduced in an antibiotic-free mouse UTI model. The in vivo generation of hypomucoid variants was primarily associated with defective or low expression of rmpADC or capsule synthesis gene wcaJ, mediated by ISKpn26 insertion/deletion or base-pair insertion. The spontaneous hypomucoid variants also outcompeted hypermucoid bacteria in the mouse urinary tract. Collectively, the ISKpn26-associated mucoid switch in CR-hvKp signifies the antibiotic-independent host adaptive evolution, providing insights into the role of mucoid switch in the persistence of CR-hvKp.

Virulence factors of Salmonella spp. isolated from free-living grass snakes Natrix natrix

Salmonellosis associated with reptiles is a well-researched topic, particularly in China and the United States, but it occurs less frequently in Europe. The growth of the human population and changes in the environment could potentially increase the interaction between humans and free-living reptiles, which are an unidentified source of Salmonella species. In this study, we sought to explore this issue by comparing the microbiota of free-living European grass snakes, scientifically known as Natrix natrix, with that of captive banded water snakes, or Nerodia fasciata. We were able to isolate 27 strains of Salmonella species from cloacal swabs of 59 N. natrix and 3 strains from 10 N. fasciata. Our findings revealed that free-living snakes can carry strains of Salmonella species that are resistant to normal human serum (NHS). In contrast, all the Salmonella species strains isolated from N. fasciata were sensitive to the action of the NHS, further supporting our findings. We identified two serovars from N. natrix: Salmonella enterica subspecies diarizonae and S. enterica subspecies houtenae. Additionally, we identified three different virulotypes (VT) with invA, sipB, prgH, orgA, tolC, iroN, sitC, sifA, sopB, spiA, cdtB and msgA genes, and β-galactosidase synthesised by 23 serovars. The identification of Salmonella species in terms of their VT is a relatively unknown aspect of their pathology. This can be specific to the serovar and pathovar and could be a result of adaptation to a new host or environment.

Ocimum basilicum and Lagenaria siceraria Loaded Lignin Nanoparticles as Versatile Antioxidant, Immune Modulatory, Anti-Efflux, and Antimicrobial Agents for Combating Multidrug-Resistant Bacteria and Fungi

Lignin nanoparticles emerged as a promising alternative for drug delivery systems owing to their biodegradability and bioactive properties. This study investigated the antimicrobial activity of the ethanolic extract of Ocimum basilicum-loaded lignin nanoparticles (OB-LNPs) and Lagenaria siceraria seed oil-loaded lignin nanoparticles (LS-LNPs) to find a solution for antimicrobial resistance. OB-LNPs and LS-LNPs were tested for their antimicrobial potential against Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae, Staphylococcus aureus, Salmonella enterica, Trichophyton mentagrophytes, Trichophyton rubrum, and Microsporum canis. OB-LNPs and LS-LNPs were further tested for their anti-efflux activity against ciprofloxacin-resistant Salmonella enterica strains and for treating Salmonella infection in a rat model. We also investigated the antifungal efficacy of OB-LNPs and LS-LNPs for treating T. rubrum infection in a guinea pig model. Both OB-LNPs and LS-LNPs showed strong antimicrobial potential against S. Typhimurium and T. rubrum infections. LS-LNPs showed antibacterial activity against Salmonella enterica species with a MIC range of 0.5-4 µg/mL and antifungal activity against T. rubrum with a MIC range of 0.125-1 µg/mL. OB-LNPs showed antibacterial activity against Salmonella enterica species with a MIC range of 0.5-2 µg/mL and antifungal activity against T. rubrum with a MIC range of 0.25-2 µg/mL. OB-LNPs and LS-LNPs downregulated the expression of ramA and acrB efflux pump genes (fold change values ranged from 0.2989 to 0.5434; 0.4601 to 0.4730 for ramA and 0.3842-0.6199; 0.5035-0.8351 for acrB). Oral administration of OB-LNPs and LS-LNPs in combination with ciprofloxacin had a significant effect on all blood parameters, as well as on liver and kidney function parameters. Oxidative stress mediators, total antioxidant capacity, and malondialdehyde were abolished by oral administration of OB-LNPs and LS-LNPs (0.5 mL/rat once daily for 5 days). Interferon-γ and tumor necrosis factor-α were also reduced in comparison with the positive control group and the ciprofloxacin-treated group. Histopathological examination of the liver and intestine of OB-LNPs and LS-LNPs-treated rats revealed an elevation in Salmonella clearance. Treatment of T. rubrum-infected guinea pigs with OB-LNPs and LS-LNPs topically in combination with itraconazole resulted in a reduction in lesion scores, microscopy, and culture results. In conclusion, OB-LNPs and LS-LNPs possess immunomodulatory and antioxidant potential and can be used as naturally derived nanoparticles for drug delivery and treatment of Salmonellosis and dermatophytosis infections.

Colistin-, cefepime-, and levofloxacin-resistant Salmonella enterica serovars isolated from Egyptian chicken carcasses

OBJECTIVES

The emergence of multidrug-resistant (MDR) Salmonella strains, especially resistant ones toward critically important antimicrobial classes such as fluoroquinolones and third- and fourth-generation cephalosporins, is a growing public health concern. The current study, therefore, aimed to determine the prevalence, and existence of virulence genes (invA, stn, and spvC genes), antimicrobial resistance profiles, and the presence of β-lactamase resistance genes (blaOXA, blaCTX-M1, blaSHV, and blaTEM) in Salmonella strains isolated from native chicken carcasses in Egypt marketed in Mansoura, Egypt, as well as spotlight the risk of isolated MDR, colistin-, cefepime-, and levofloxacin-resistant Salmonella enterica serovars to public health.

METHODS

One hundred fifty freshly dressed native chicken carcasses were collected from different poultry shops in Mansoura City, Egypt between July 2022 and November 2022. Salmonella isolation was performed using standard bacteriological techniques, including pre-enrichment in buffered peptone water (BPW), selective enrichment in Rappaport Vassiliadis broth (RVS), and cultivating on the surface of xylose-lysine-desoxycholate (XLD) agar. All suspected Salmonella colonies were subjected to biochemical tests, serological identification using slide agglutination test, and Polymerase Chain Reaction (PCR) targeting the invasion A gene (invA; Salmonella marker gene). Afterward, all molecularly verified isolates were screened for the presence of virulence genes (stn and spvC). The antimicrobial susceptibility testing for isolated Salmonella strains towards the 16 antimicrobial agents tested was analyzed by Kirby-Bauer disc diffusion method, except for colistin, in which the minimum inhibition concentration (MIC) was determined by broth microdilution technique. Furthermore, 82 cefotaxime-resistant Salmonella isolates were tested using multiplex PCR targeting the β-lactamase resistance genes, including blaOXA, blaCTX-M1, blaSHV, and blaTEM genes.

RESULTS

Salmonella enterica species were molecularly confirmed via the invA Salmonella marker gene in 18% (27/150) of the freshly dressed native chicken carcasses. Twelve Salmonella serotypes were identified among 129 confirmed Salmonella isolates with the most predominant serotypes were S. Kentucky, S. Enteritidis, S. Typhimurium, and S. Molade with an incidence of 19.4% (25/129), 17.1% (22/129), 17.1% (22/129), and 10.9% (14/129), respectively. All the identified Salmonella isolates (n = 129) were positive for both invA and stn genes, while only 31.8% (41/129) of isolates were positive for the spvC gene. One hundred twenty-one (93.8%) of the 129 Salmonella-verified isolates were resistant to at least three antibiotics. Interestingly, 3.9%, 14.7%, and 75.2% of isolates were categorized into pan-drug-resistant, extensively drug-resistant, and multidrug-resistant, respectively. The average MAR index for the 129 isolates tested was 0.505. Exactly, 82.2%, 82.2%, 63.6%, 51.9%, 50.4%, 48.8%, 11.6%, and 10.1% of isolated Salmonella strains were resistant to cefepime, colistin, cefotaxime, ceftazidime/clavulanic acid, levofloxacin, ciprofloxacin, azithromycin, and meropenem, respectively. Thirty-one out (37.8%) of the 82 cefotaxime-resistant Salmonella isolates were β-lactamase producers with the blaTEM as the most predominant β-lactamase resistance gene, followed by blaCTX-M1 and blaOXA genes, which were detected in 21, 16, and 14 isolates respectively).

CONCLUSION

The high prevalence of MDR-, colistin-, cefepime-, and levofloxacin-resistant Salmonella serovars among Salmonella isolates from native chicken is alarming as these antimicrobials are critically important in treating severe salmonellosis cases and boost the urgent need for controlling antibiotic usage in veterinary and human medicine to protect public health.

Whole-Genome Analysis of Extensively Drug-Resistant Enterobacter hormaechei Isolated from a Patient with Non-Hodgkin's Lymphoma

BACKGROUND

Currently, the Enterobacteriaceae species are responsible for a variety of serious infections and are already considered a global public health problem, especially in underdeveloped countries, where surveillance and monitoring programs are still scarce and limited. Analyses were performed on the complete genome of an extensively antibiotic-resistant strain of Enterobater hormaechei, which was isolated from a patient with non-Hodgkin's lymphoma, who had been admitted to a hospital in the city of Manaus, Brazil.

METHODS

Phenotypical identification and susceptibility tests were performed in automated equipment. Total DNA extraction was performed using the PureLink genomic DNA mini-Kit. The genomic DNA library was prepared with Illumina Microbial Amplicon Prep and sequenced in the MiSeq Illumina Platform. The assembly of the whole-genome and individual analyses of specific resistance genes extracted were carried out using online tools and the Geneious Prime software.

RESULTS

The analyses identified an extensively resistant ST90 clone of E. hormaechei carrying different genes, including blaCTX-M-15, blaGES-2, blaTEM-1A, blaACT-15, blaOXA-1 and blaNDM-1, [aac(3)-IIa, aac(6')-Ian, ant(2″)-Ia], [aac(6')-Ib-cr, (qnrB1)], dfrA25, sul1 and sul2, catB3, fosA, and qnrB, in addition to resistance to chlorhexidine, which is widely used in patient antisepsis.

CONCLUSIONS

These findings highlight the need for actions to control and monitor these pathogens in the hospital environment.

Emergence of plasmid-mediated tigecycline resistance tet(X4) gene in Enterobacterales isolated from wild animals in captivity

Background

Over the past few decades, antimicrobial resistance (AMR) has emerged as a global health challenge in human and veterinary medicine. Research on AMR genes in captive wild animals has increased. However, the presence and molecular characteristics of tet(X)-carrying bacteria in these animals remain unknown.

Methods

Eighty-four samples were collected from captive wild animals. tet(X) variants were detected using polymerase chain reaction and the isolates were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. All isolated strains were subjected to antimicrobial susceptibility testing and whole-genome sequencing. The virulence of an Escherichia coli strain carrying enterotoxin genes was assessed using a Galleria mellonella larval model.

Results

We isolated two tet(X4)-positive E. coli strains and one tet(X4)-positive Raoultella ornithinolytica strain. Antimicrobial susceptibility tests revealed that all three tet(X4)-carrying bacteria were sensitive to the 13 tested antimicrobial agents, but exhibited resistance to tigecycline. Notably, one tet(X4)-carrying E. coli strain producing an enterotoxin had a toxic effect on G. mellonella larvae. Whole-genome sequencing analysis showed that the two tet(X4)-carrying E. coli strains had more than 95% similarity to tet(X4)-containing E. coli strains isolated from pigs and humans in China.

Conclusion

The genetic environment of tet(X4) closely resembled that of the plasmid described in previous studies. Our study identified tet(X4)-positive strains in wildlife and provided valuable epidemiological data for monitoring drug resistance. The identification of enterotoxin-producing E. coli strains also highlights the potential risks posed by virulence genes.

Transcriptional responses of cytokines, immunoglobulin A, and nitric oxide genes in 1-day-old chicks post Salmonella typhimurium infection: An experimental study

Background

Salmonella has become one of the hazards prevalent foodborne pathogens causing different diseases in chickens. However, Salmonella typhimurium (ST), a nonhost-specific serovar, is a major avian agent that causes severe disturbance in young chicken wellness.

Aim

The occurrence of Salmonella in chickens and their antimicrobial resistance were explored in this study. In addition, the immune response of 1-day-old broiler chicks, against multidrug resistant (MDR) ST infection, was also assessed at 4 and 24 hours post infection (pi) in the cecum and spleen, representing their mucosal and systemic immune responses, respectively.

Methods

A total of 375 samples from 130 diseased and apparently healthy broiler and layer chickens were randomly collected for Salmonella isolation, identification, and resistance profile evaluation, from farms and different clinical laboratories. The immune response of 1-day-old broiler chicks, Ross 308, against in-vivo ST infection was ascertained through the evaluation of heterophile phagocytosis and s expression of cytokines, immunoglobulin A and other immune-regulating genes in the cecum and spleen. Twenty-four, 1-day-old nonvaccinated broiler chicks were used and divided into two groups. The chicks in the infected group were orally inoculated with 0.5 ml of 2 × 108 colony forming units (CFU)/ml of MDR ST suspension, while those in the control group were taken nutrient broth.

Results

Seven out of 130 (5.38%) examined chickens were positive for Salmonella. All isolates (100%) were resistant to amoxicillin-clavulanic acid (AMC), cefazolin (CZ), cefoxitin (FOX), ciprofloxacin (CIP), nalidixic acid (NA), tetracycline (TE), fosfomycin (FOS), and colistin (CT) with multiple antimicrobial resistances (MARs) index range of 0.72-0.83, where none of them was resistant to meropenem (MEM). The results of immune response revealed that chicks infected with ST showed significantly different phagocytosis percentages and index values compared to controls. According to the real-time quantitative polymerase chain reaction (RT-qPCR) results, the transcription of IL-8, iNOS, IL-18, IgA, and IFN-γ for chicks infected by ST showed a significantly increased trend (p < 0.01) with increasing chicken age and was higher in the cecum than spleen compared to controls (p < 0.05) during 24 hours after infection.

Conclusion

The findings indicated a strong mucosal immune response in the chicks after the ST challenge, which reflects humoral and cellular responses. Our insight recommended the occurrence of a natural immune response stimulator at 1 day age to face the infection, and this can prevent the resistance transfer, with efficient control measures.

Outer Membrane Proteins and Efflux Pumps Mediated Multi-Drug Resistance in Salmonella: Rising Threat to Antimicrobial Therapy

Despite colossal achievements in antibiotic therapy in recent decades, drug-resistant pathogens have remained a leading cause of death and economic loss globally. One such WHO-critical group pathogen is Salmonella. The extensive and inappropriate treatments for Salmonella infections have led from multi-drug resistance (MDR) to extensive drug resistance (XDR). The synergy between efflux-mediated systems and outer membrane proteins (OMPs) may favor MDR in Salmonella. Differential expression of the efflux system and OMPs (influx) and positional mutations are the factors that can be correlated to the development of drug resistance. Insights into the mechanism of influx and efflux of antibiotics can aid in developing a structurally stable molecule that can be proficient at escaping from the resistance loops in Salmonella. Understanding the strategic responsibilities and developing policies to address the surge of drug resistance at the national, regional, and global levels are the needs of the hour. In this Review, we attempt to aggregate all the available research findings and delineate the resistance mechanisms by dissecting the involvement of OMPs and efflux systems. Integrating major OMPs and the efflux system's differential expression and positional mutation in Salmonella may provide insight into developing strategic therapies for one health application.

The Impact of Bamboo Consumption on the Spread of Antibiotic Resistance Genes in Giant Pandas

The spread of antibiotic resistance genes (ARGs) in the environment exacerbates the contamination of these genes; therefore, the role plants play in the transmission of resistance genes in the food chain requires further research. Giant pandas consume different bamboo parts at different times, which provides the possibility of investigating how a single food source can affect the variation in the spread of ARGs. In this study, metagenomic analysis and the Comprehensive Antibiotic Resistance Database (CARD) database were used to annotate ARGs and the differences in gut microbiota ARGs during the consumption of bamboo shoots, leaves, and culms by captive giant pandas. These ARGs were then compared to investigate the impact of bamboo part consumption on the spread of ARGs. The results showed that the number of ARGs in the gut microbiota of the subjects was highest during the consumption of bamboo leaves, while the variety of ARGs was highest during the consumption of shoots. Escherichia coli, which poses a higher risk of ARG dissemination, was significantly higher in the leaf group, while Klebsiella, Enterobacter, and Raoultella were significantly higher in the shoot group. The ARG risk brought by bamboo shoots and leaves may originate from soil and environmental pollution. It is recommended to handle the feces of giant pandas properly and regularly monitor the antimicrobial and virulence genes in their gut microbiota to mitigate the threat of antibiotic resistance.

Resistance profiles, virulence and antimicrobial resistance genes of XDR S. Enteritidis and S. Typhimurium

Avian salmonellosis is concomitant with high financial crises in the poultry industry as well as food-borne illness in man. The present study is designed to investigate the emergence of Salmonella Enteritidis and Salmonella Typhimurium in diseased broilers, resistance profiles, and monitoring virulence and antibiotic resistance genes. Consequently, 450 samples (cloacal swabs, liver, and spleen) were collected from 150 diseased birds from different farms in Giza Governorate, Egypt. Subsequently, the bacteriological examination was done. Afterward, the obtained Salmonella isolates were tested for serogrouping, antibiogram, PCR monitoring of virulence (invA, stn, hilA, and pefA), and antimicrobial resistance genes (blaTEM, blaCTX-M, blaNDM, ermA, sul1, tetA, and aadA1). The total prevalence of Salmonella in the examined diseased broilers was 9.3%, and the highest prevalence was noticed in cloacal swabs. Among the recovered Salmonella isolates (n = 35), 20 serovars were recognized as S. Enteritidis and 15 serovars were identified as S. Typhimurium. Almost 60% of the retrieved S. Enteritidis serovars were extensively drug-resistant (XDR) to seven antimicrobial classes and inherited sul1, blaTEM, tetA, blaCTX-M, ereA, and aadA1 genes. Likewise, 25% of the recovered S. Enteritidis serovars were multidrug-resistant (MDR) to six classes and have sul1, blaTEM, tetA, blaCTX-M, and ereA resistance genes. Also, 66.7% of the retrieved S. Typhimurium serovars were XDR to seven classes and have sul1, blaTEM, tetA, blaCTX-M, ereA, and aadA1 genes. Succinctly, this report underlined the reemergence of XDR S. Typhimurium and S. Enteritidis in broiler chickens. Meropenem and norfloxacin exposed a hopeful antimicrobial activity toward the re-emerging XDR S. Typhimurium and S. Enteritidis in broilers. Moreover, the recurrence of these XDR Salmonella strains poses a potential public health threat.

Clinical Characteristics, Antimicrobial Resistance, Virulence Genes and Multi-Locus Sequence Typing of Non-Typhoidal Salmonella Serovar Typhimurium and Enteritidis Strains Isolated from Patients in Chiang Mai, Thailand

Non-typhoidal salmonellosis (NTS) caused by ingesting Salmonella enterica contaminated food or drink remains a major bacterial foodborne disease. Clinical outcomes of NTS range from self-limited gastroenteritis to life-threatening invasive NTS (iNTS). In this study, we isolated Salmonella spp. from the stool and blood of patients hospitalized at Maharaj Nakorn Chiang Mai Hospital, Chiang Mai, Thailand, between 2016-2021 (a total of 395 cases). Then, serovar Typhimurium and Enteritidis were identified and further characterized by multiplex PCR, and multi-locus sequence typing. Our data show that multidrug resistance (MDR) sequence type 34 (ST34) and ST11 are the predominant sequence types for serovars Typhimurium and Enteritidis, respectively. Most S. Typhimurium ST34 lacks spvB, and most S. Enteritidis ST11 harbor sseI, sodCI, rpoS and spvB genes. NTS can be found in a wide range of ages, and anemia could be a significant factor for S. Typhimurium infection (86.3%). Both S. Typhimurium (6.7%) and S. Enteritidis (25.0%) can cause iNTS in immunocompromised patients. S. Typhimurium conferred MDR phenotype higher than S. Enteritidis with multiple antibiotic resistance indexes of 0.22 and 0.04, respectively. Here, we characterized the important S. Typhimurium, S. Enteritidis, and human clinical factors of NTS within the region.

Multidrug-Resistant Salmonella Species and Their Mobile Genetic Elements from Poultry Farm Environments in Malaysia

The prevalence and persistent outbreaks of multidrug-resistant (MDR) Salmonella in low-income countries have received growing attention among the public and scientific community. Notably, the excessive use of antibiotics in chicken feed for the purpose of treatment or as prophylaxis in the poultry industry have led to a rising rate of antimicrobial resistance. Therefore, this study aimed to determine the presence of antimicrobial-resistant Salmonella species and its mobile genetic elements from soil and effluent samples of 33 randomly selected poultry farms in Selangor, Malaysia. Salmonella species were isolated on selective media (CHROMagar™ Salmonella). VITEK® 2 system was used to identify the isolates and their antimicrobial susceptibility. Subsequently, eight isolates were subjected to the whole genome sequencing (WGS). Based on the results, Salmonella spp. was detected in 38.1% (24/63) of samples, with the highest resistance to ampicillin (62.5%), followed by ampicillin/sulbactam (50.0%) and ciprofloxacin (45.8%). Meanwhile, the identified serovars were Salmonella enterica subspecies enterica serovar Weltevreden (S. Weltevreden), S. Jedburgh, and S. Brancaster. The most prevalent resistance genes detected include qnrS1, blaTEM-176, dfrA14, and tet(A). The IncX1 plasmid, with encoded resistance genes, was also detected in four isolates. Furthermore, mutations in the quinolone resistant-determining regions (QRDR) were discovered, specifically in the gyrA, gyrB, and parC genes. In short, surveillance such as continuous monitoring of antimicrobial resistance and emerging trends in resistance patterns through farm environmental samples could provide information to formulate public health interventions for effective infection prevention and disease control.

Excessive disinfection aggravated the environmental prevalence of antimicrobial resistance during COVID-19 pandemic

During COVID-19 pandemic, chemicals from excessive consumption of pharmaceuticals and disinfectants i.e., antibiotics, quaternary ammonium compounds (QACs), and trihalomethanes (THMs), flowed into the urban environment, imposing unprecedented selective pressure to antimicrobial resistance (AMR). To decipher the obscure character pandemic-related chemicals portrayed in altering environmental AMR, 40 environmental samples covering water and soil matrix from surroundings of Wuhan designated hospitals were collected on March 2020 and June 2020. Chemical concentrations and antibiotic resistance gene (ARG) profiles were revealed by ultra-high-performance liquid chromatography-tandem mass spectrometry and metagenomics. Selective pressure from pandemic-related chemicals ascended by 1.4-5.8 times in March 2020 and then declined to normal level of pre-pandemic period in June 2020. Correspondingly, the relative abundance of ARGs under increasing selective pressure was 20.1 times that under normal selective pressure. Moreover, effect from QACs and THMs in aggravating the prevalence of AMR was elaborated by null model, variation partition and co-occurrence network analyses. Pandemic-related chemicals, of which QACs and THMs respectively displayed close interaction with efflux pump genes and mobile genetic elements, contributed >50 % in shaping ARG profile. QACs bolstered the cross resistance effectuated by qacEΔ1 and cmeB to 3.0 times higher while THMs boosted horizon ARG transfer by 7.9 times for initiating microbial response to oxidative stress. Under ascending selective pressure, qepA encoding quinolone efflux pump and oxa-20 encoding β-lactamases were identified as priority ARGs with potential human health risk. Collectively, this research validated the synergistic effect of QACs and THMs in exacerbating environmental AMR, appealing for the rational usage of disinfectants and the attention for environmental microbes in one-health perspective.

Prevalence and Characterization of Salmonella Isolated from Chickens in Anhui, China

Salmonella is one of the most important zoonotic pathogens that can cause both acute and chronic illnesses in poultry flocks, and can also be transmitted to humans from infected poultry. The purpose of this study was to investigate the prevalence, antimicrobial resistance, and molecular characteristics of Salmonella isolated from diseased and clinically healthy chickens in Anhui, China. In total, 108 Salmonella isolates (5.66%) were successfully recovered from chicken samples (n = 1908), including pathological tissue (57/408, 13.97%) and cloacal swabs (51/1500, 3.40%), and S. Enteritidis (43.52%), S. Typhimurium (23.15%), and S. Pullorum (10.19%) were the three most prevalent isolates. Salmonella isolates showed high rates of resistance to penicillin (61.11%), tetracyclines (47.22% to tetracycline and 45.37% to doxycycline), and sulfonamides (48.89%), and all isolates were susceptible to imipenem and polymyxin B. In total, 43.52% isolates were multidrug-resistant and had complex antimicrobial resistance patterns. The majority of isolates harbored cat1 (77.78%), blaTEM (61.11%), and blaCMY-2 (63.89%) genes, and the antimicrobial resistance genes in the isolates were significantly positively correlated with their corresponding resistance phenotype. Salmonella isolates carry high rates of virulence genes, with some of these reaching 100% (invA, mgtC, and stn). Fifty-seven isolates (52.78%) were biofilm-producing. The 108 isolates were classified into 12 sequence types (STs), whereby ST11 (43.51%) was the most prevalent, followed by ST19 (20.37%) and ST92 (13.89%). In conclusion, Salmonella infection in chicken flocks is still serious in Anhui Province, and not only causes disease in chickens but might also pose a threat to public health security.

Exploring broilers and native fowls of Andaman and Nicobar Islands as a source of β-lactamase-producing Enterobacteriaceae even with limited anthropogenic activities and docking-based identification of catalytic domains in novel β-lactamase variants

Objectives

The present study was conducted to detect the occurrence of β-lactamase and biofilm-producing Escherichia coli, Salmonella, and Klebsiella in broilers and native fowl reared in the Andaman and Nicobar Islands, India. The study also included molecular docking experiments to confirm the nature of the catalytic domains found in the β-lactamase variants obtained and to reveal the clonal relationship of the isolates with human clinical strains from the database.

Materials and methods

A total of 199 cloacal swabs were collected from five poultry breeds/varieties (broiler, Vanraja, Desi, Nicobari, and layer) in three districts of the Andaman and Nicobar Islands. E. coli, Salmonella enterica, and Klebsiella pneumoniae were isolated by standard techniques and confirmed by PCR. Phenotypical β-lactamase producers were identified by a double-disc test. The genes (bla _CTX, bla _SHV, bla _TEM , and bla _AmpC) were screened, and selected sequences of β-lactamase variants were submitted to DDBJ. Homology modeling, model validation, and active site identification of different β-lactamase variants were done by the SWISS-MODEL. Molecular docking was performed to identify the catalytic domains of the β-lactamase variants. The selected β-lactamase sequences were compared with the Indian ESBL sequences from human clinical strains in NCBI-GenBank.

Results

In total, 425 Enterobacteriaceae strains were isolated from the collected samples. Klebsiella pneumoniae (42.58%) was found to be the most prevalent, followed by Salmonella enterica (30.82%) and E. coli (26.58%). The phenotypical antibiogram of all 425 isolates showed the highest resistance against oxytetracycline (61-76%) and the lowest against gentamicin (15-20%). Phenotypical production of β-lactamase enzymes was observed in 141 (33.38%) isolates. The isolation rate of β-lactamase producing E. coli, Salmonella enterica, and Klebsiella pneumoniae was significantly higher (p < 0.05) in the birds reared in the South Andaman district (25.6, 17.5, and 18.7%, respectively) than in Nicobar (11.5, 7.6, 7.1%, respectively). Genotyping of the β-lactamase-producing isolates revealed the maximum possession of bla _TEM, followed by bla _SHV and bla _{CTX - M}. The nucleotide sequences were found to be similar with bla _{CTX - M-15}, bla _{SHV - 11}, bla _{SHV - 27}, bla _{SHV - 228}, bla _{TEM - 1}, and bla _AmpC in BLAST search. Distribution of studied biofilm-associated genes in Enterobacteriaceae strains from different varieties of the birds revealed that the layer birds had the maximum possession, followed by Vanraja, Desi, broilers, and Nicobari fowls. The phylogenetic analysis of selected sequences revealed a partial clonal relationship with human clinical strains of the Indian subcontinent. Molecular docking depicted the Gibbs free energy release for 10 different macromolecules (proteins) and ligand (antibiotic) complexes, ranging from -8.1 (SHV-27 + cefotaxime) to -7 (TEM-1 + cefotaxime) kcal/mol.

Conclusion and relevance

The study revealed β-lactamase variants circulating in the fowl population of the Andaman and Nicobar Islands (India), even in remote places with low anthropogenic activity. Most of the strains possessed bla _{TEM - 1}, followed by bla _{CTX - M-15}. Possession of bla _{SHV - 11}, bla _{SHV - 27}, and bla _{SHV - 228} in poultry Enterobacteriaceae strains was not reported earlier from any part of the world. The phylogenetic analysis revealed a partial clonal relationship of β-lactamase sequences with the human clinical strains isolated from the Indian subcontinent.

Bioactive metabolites of Streptomyces misakiensis display broad-spectrum antimicrobial activity against multidrug-resistant bacteria and fungi

Background

Antimicrobial resistance is a serious threat to public health globally. It is a slower-moving pandemic than COVID-19, so we are fast running out of treatment options.

Purpose

Thus, this study was designed to search for an alternative biomaterial with broad-spectrum activity for the treatment of multidrug-resistant (MDR) bacterial and fungal pathogen-related infections.

Methods

We isolated Streptomyces species from soil samples and identified the most active strains with antimicrobial activity. The culture filtrates of active species were purified, and the bioactive metabolite extracts were identified by thin-layer chromatography (TLC), preparative high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR) spectroscopy, and gas chromatography-mass spectrometry (GC-MS). The minimum inhibitory concentrations (MICs) of the bioactive metabolites against MDR bacteria and fungi were determined using the broth microdilution method.

Results

Preliminary screening revealed that Streptomyces misakiensis and S. coeruleorubidus exhibited antimicrobial potential. The MIC₅₀ and MIC₉₀ of S. misakiensis antibacterial bioactive metabolite (ursolic acid methyl ester) and antifungal metabolite (tetradecamethylcycloheptasiloxane) against all tested bacteria and fungi were 0.5 μg/ml and 1 μg/mL, respectively, versus S. coeruleorubidus metabolites: thiocarbamic acid, N,N-dimethyl, S-1,3-diphenyl-2-butenyl ester against bacteria (MIC₅₀: 2 μg/ml and MIC₉₀: 4 μg/mL) and fungi (MIC₅₀: 4 μg/ml and MIC₉₀: 8 μg/mL). Ursolic acid methyl ester was active against ciprofloxacin-resistant strains of Streptococcus pyogenes, S. agalactiae, Escherichia coli, Klebsiella pneumoniae, and Salmonella enterica serovars, colistin-resistant Aeromonas hydrophila and K. pneumoniae, and vancomycin-resistant Staphylococcus aureus. Tetradecamethylcycloheptasiloxane was active against azole- and amphotericin B-resistant Candida albicans, Cryptococcus neoformans, C. gattii, Aspergillus flavus, A. niger, and A. fumigatus. Ursolic acid methyl ester was applied in vivo for treating S. aureus septicemia and K. pneumoniae pneumonia models in mice. In the septicemia model, the ursolic acid methyl ester-treated group had a significant 4.00 and 3.98 log CFU/g decrease (P < 0.05) in liver and spleen tissue compared to the infected, untreated control group. Lung tissue in the pneumonia model showed a 2.20 log CFU/g significant decrease in the ursolic acid methyl ester-treated group in comparison to the control group. The haematological and biochemical markers in the ursolic acid methyl ester-treated group did not change in a statistically significant way. Moreover, no abnormalities were found in the histopathology of the liver, kidneys, lungs, and spleen of ursolic acid methyl ester-treated mice in comparison with the control group.

Conclusion

S. misakiensis metabolite extracts are broad-spectrum antimicrobial biomaterials that can be further investigated for the potential against MDR pathogen infections. Hence, it opens up new horizons for exploring alternative drugs for current and reemerging diseases.

Review of major meat-borne zoonotic bacterial pathogens

The importance of meat-borne pathogens to global disease transmission and food safety is significant for public health. These pathogens, which can cause a variety of diseases, include bacteria, viruses, fungi, and parasites. The consumption of pathogen-contaminated meat or meat products causes a variety of diseases, including gastrointestinal ailments. Humans are susceptible to several diseases caused by zoonotic bacterial pathogens transmitted through meat consumption, most of which damage the digestive system. These illnesses are widespread worldwide, with the majority of the burden borne by developing countries. Various production, processing, transportation, and food preparation stages can expose meat and meat products to bacterial infections and/or toxins. Worldwide, bacterial meat-borne diseases are caused by strains of Escherichia coli, Salmonella, Listeria monocytogenes, Shigella, Campylobacter, Brucella, Mycobacterium bovis, and toxins produced by Staphylococcus aureus, Clostridium species, and Bacillus cereus. Additionally, consuming contaminated meat or meat products with drug-resistant bacteria is a severe public health hazard. Controlling zoonotic bacterial pathogens demands intervention at the interface between humans, animals, and their environments. This review aimed to highlight the significance of meat-borne bacterial zoonotic pathogens while adhering to the One Health approach for creating efficient control measures.

Antimicrobial Resistance of Salmonella Strains Isolated from Human, Wild Boar, and Environmental Samples in 2018-2020 in the Northwest of Italy

Antimicrobial resistance is one of the most challenging public health problems worldwide, and integrated surveillance is a key aspect in a One Health control strategy. Additionally, Salmonella is the second most common zoonosis in Europe. We aimed to investigate the circulation of Salmonella strains and their related antimicrobial resistance in human, environmental, and wild boar samples from the northwest of Italy, from 2018 to 2020, to obtain a more comprehensive epidemiological picture. Salmonella Typhimurium 1,4,[5],12:i:-, S. Veneziana and S. Newport were the most common serotypes occurring in humans, the environment, and wild boar, respectively. Antimicrobial resistance was rather common in Salmonella isolates, with those from human displaying the highest degree of resistance against sulfadiazine−sulfamerazine−sulfamethazine (>90% of resistance). Moreover, resistance against azithromycin were exclusively observed in environmental samples, while only 7.7% (95% CI = 1.6−20.8) of wild boar isolates experienced resistance against trimethoprim−sulfamethoxazole. Multidrug resistance concurrently involved up to seven antimicrobial classes in human isolates, including third-generation cephalosporins and fluoroquinolones. Salmonella Typhimurium in humans and serotypes Goldcoast and Rissen from environmental sources showed the highest levels of resistance. This study shows diverse antimicrobial resistance patterns in Salmonella strains isolated from different sources and gives a broad picture of antimicrobial resistance spread in wild animals, humans, and the environment.

Physiological Characteristics of Putative Enterobacteria Associated with Meat and Fish Available in Southern Brazilian Retail Markets: Antimicrobial Susceptibility, Toxic Metal Tolerance and Expression of Efflux Pumps

Multidrug-resistant (MDR) mesophilic facultatively anaerobic Gram-negative rods are a public health issue and their spread from animal-source foods to humans is of concern worldwide. Hence, the aim of this study was to examine the antibiotic susceptibility patterns and physiological aspects of such rods, including their tolerance to toxic metals and the screening of efflux pumps expressing isolates among enterobacteria isolated from meat (chicken, beef and pork) and fish samples acquired from retail establishments in a Brazilian urban Centre of over 2,300,000 inhabitants. The study revealed that 62.9% of isolated bacteria were resistant to at least one antimicrobial, of which 32.3% and 8.1% were resistant to one and two of the tested drugs, respectively. A resistance of up to six antimicrobials was also observed (0.9%). Out of the total amount, 22.7% were classified as MDR. Chicken was the meat that harbored most MDR isolates, and fish harbored the least. It was not possible to distinguish the different types of meat or fish considering the resistance patterns. The MDR isolates showed a higher tolerance to mercury and cadmium salts and the increased activity of the efflux mechanisms compared to other susceptible or resistant strains. In One Health. the perspective occurrence of putative MDR bacteria in fresh meat and fish draws attention to the antimicrobial resistance phenomenon in an open environment.

Regulatory Mechanisms between Quorum Sensing and Virulence in Salmonella

Salmonella is a foodborne pathogen that causes enterogastritis among humans, livestock and poultry, and it not only causes huge economic losses for the feed industry but also endangers public health around the world. However, the prevention and treatment of Salmonella infection has remained poorly developed because of its antibiotic resistance. Bacterial quorum sensing (QS) system is an intercellular cell-cell communication mechanism involving multiple cellular processes, especially bacterial virulence, such as biofilm formation, motility, adherence, and invasion. Therefore, blocking the QS system may be a new strategy for Salmonella infection independent of antibiotic treatment. Here, we have reviewed the central role of the QS system in virulence regulation of Salmonella and summarized the most recent advances about quorum quenching (QQ) in virulence attenuation during Salmonella infection. Unraveling the complex relationship between QS and bacterial virulence may provide new insight into the therapy of pathogen infection.

Antibacterial activity of bioactive compounds extracted from red kidney bean (Phaseolus vulgaris L.) seeds against multidrug-resistant Enterobacterales

In the present study, biologically active compounds such as phenolic-rich extract (PRE), 7S globulin (vicilin), and 11S globulin (legumin) from red kidney bean (Phaseolus vulgaris L.) seeds were extracted and evaluated as antibacterial agents against multidrug-resistant (MDR) Enterobacterales isolated from both animal and human sources. The overall occurrence rate of Enterobacterales was 43.6%, which significantly differed between animal (38.75%) and human (56.67%) sources. Antimicrobial susceptibility testing revealed that Enterobacterales isolates exhibited full resistance (100%) to amoxicillin-clavulanic acid, followed by ampicillin (75.44%), erythromycin (71.93%), cefoxitin (70.18%), amoxicillin (66.66%), ceftriaxone (64.91%), and trimethoprim/sulfamethoxazole (56.14%). Worthy of note, 97.92% of Enterobacterales isolates were MDR. The total phenolic contents (TPC; 53 ± 2 mg GAE g-1) and total flavonoid contents (TFC; 26 ± 1 mg QE g-1) were recorded. The major phenolic and flavonoid components were catechol (17.63 μg/mL) and hesperidin (11.37 μg/mL), respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was performed to detect the 7S and 11S globulin‘s molecular mass. The data revealed that red kidney bean protein isolate (KPI) includes two major portions: 7S and 11S globulins. The bioactive compounds of Phaseolus vulgaris were investigated for their antibacterial activities against Enterobacterales for the first time. The protein component (MIC = 0.125 – 2 μg/mL; 53.85%) and its 7S and 11S globulin subunits (MIC = 0.5 – 2 μg/mL; 30.77% each) were the most potent extracts, whereas the methanolic extract was the least effective one (MIC = 2 μg/mL; 15.38%). The results displayed the potential of protein bioactive compounds as a hopeful candidate for enhancing future medication plans for the treatment of Enterobacterales originating from animal and human sources.

Protective effects of E. coli Nissle 1917 on chickens infected with Salmonella pullorum

The probiotic E. coli Nissle 1917 (EcN) plays an important role in regulating the microbial components of the gut and preventing inflammation of the gastrointestinal tract. Currently, the long-term use of antibiotics for the treatment of lethal white diarrhea in chicks caused by Salmonella has led to increased morbidity and mutation rates. Therefore, we want to use EcN as an antibiotic alternative as an alternative approach to prevent Salmonella-induced white diarrhea in chickens. To date, there are no reports of EcN being used for the prevention and control of Salmonella pullorum (S. pullorum) in chickens. In vitro, pretreatment with EcN significantly decreased the cellular invasion of S. pullorum CVCC533 in a chicken fibroblast (DF-1) cell model. Then, 0-day-old egg-laying chickens were orally inoculated with EcN at a dose of 10⁹ CFU/100 μL at either Day 1 (EcN1) or both Day 1 and Day 4 (EcN2). Then, S. pullorum CVCC533 was used to challenge the cells at a dose of 1.0 × 10⁷ CFU/100 μL on Day 8. Next, the body weights and survival rates were recorded for 14 consecutive days, and the colonization of S. pullorum in the spleen and liver at 7 days post-challenge (dpc) was determined. Chicken feces were also collected at 2, 4, 6 and 8 dpc to evaluate the excretion of pathogenic bacteria in feces. The liver, duodenum and rectum samples were collected and analyzed by pathological histology at 7 dpc to evaluate the protective effect of EcN on the mucosa, villi and crypts of the small intestine. The spleen and bursa were collected, and the immune organ index was calculated. In addition, the contents of the cecum of chicks were collected at 7 dpc for 16S rRNA sequencing to detect the distribution of microbial communities in the intestine. The results showed that EcN was able to protect against CVCC533 challenge, as shown by decreased body weight loss, mortality and shedding of pathogenic bacteria in fecal samples in the EcN1 plus Salmonella challenge group (EcN1S) but not the EcN2 plus Salmonella challenge group (EcN2S). The pathogenic changes in the liver, duodenum and rectum also demonstrated that one dose but not two doses of EcN effectively prolonged the length of the pilus with decreased crypt depth, indicating its protective effects against S. pullorum. In addition, the 16S rRNA sequencing results suggested that EcN could enlarge the diversity of intestinal flora, decrease the abundance of pathogenic bacteria and increase the abundance of beneficial bacteria, such as Lactobacillus. In conclusion, EcN has shown moderate protection against S. pullorum challenge in chickens.

Rapid Detection of Salmonella spp from Meat: Loop Mediated Isothermal Amplification (LAMP)

Loop-mediated isothermal amplification (LAMP) is a novel, high specific and sensitive method which amplifies nucleic acid under isothermal conditions. Salmonella is considered one of the threatening pathogens in food industries and these species are associated with distinct food poisoning called salmonellosis. Four primers (two outer and two inner primers) were designed to target six distinct regions on the target gene invA which is conserved in Salmonella species. The reaction was optimised for 60 mins at 65 ̊C. The sensitivity of the LAMP and PCR assay for Salmonella was 10 CFU/ml and 100 CFU/ml respectively. Artificial spiking of chicken meat shows detection of Salmonella even at dilution to extinction (<1 CFU/ml) immediately after spiking as well after 48hr enrichment. All the LAMP experiments were compared to PCR method. This study reports the development of a highly sensitive, specific and a rapid diagnostic assay for the detection of Salmonella from food. The developed method could be very useful for routine pathogens point of care (POC) diagnostics.

Antimicrobial resistance of Escherichia coli, Enterobacter spp., Klebsiella pneumoniae and Enterococcus spp. isolated from the feces of giant panda

Background

Escherichia coli, Enterobacter spp., Klebsiella pneumoniae and Enterococcus spp., common gut bacteria in giant pandas, include opportunistic pathogens. The giant panda is an endangered species, classified as vulnerable by the World Wildlife Foundation. Continuous monitoring for the emergence of antimicrobial resistance (AMR) among bacterial isolates from giant pandas is vital not only for their protection but also for public health.

Results

A total of 166 E. coli, 68 Enterobacter spp., 116 K. pneumoniae and 117 Enterococcus spp. isolates were collected from fecal samples of 166 giant pandas. In the antimicrobial susceptibility tests, 144 E. coli isolates, 66 Enterobacter spp. isolates, 110 K. pneumoniae isolates and 43 Enterococcus spp. isolates were resistant to at least one antimicrobial. The resistant isolates carried antimicrobial resistance genes (ARGs), including sul3, bla_TEM, bla_SHV and tetA. The differences in the prevalence of the bla types implied that the genetic basis for β-lactam resistance among the E. coli, Enterobacter spp. and K. pneumoniae isolates was different. The strain K. pneumoniae K85 that was resistant to sixteen antimicrobials was selected for whole genome sequencing. The genome contained Col440I, IncFIB_K and IncFII_K plasmids and altogether 258 ARGs were predicted in the genome; 179 of the predicted ARGs were efflux pump genes. The genetic environment of the β-lactamase genes bla_CTX-M-3 and bla_TEM-1 in the K. pneumoniae K85 genome was relatively similar to those in other sequenced K. pneumoniae genomes. In comparing the giant panda age groups, the differences in the resistance rates among E. coli, K. pneumoniae and Enterobacter spp. isolates suggested that the infections in giant pandas of different age should be treated differently.

Conclusions

Antimicrobial resistance was prevalent in the bacterial isolates from the giant pandas, implying that the gut bacteria may pose serious health risks for captive giant pandas. The resistance genes in the genome of K. pneumoniae K85 were associated with insertion sequences and integron-integrase genes, implying a potential for the further spread of the antimicrobial resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02514-0.

Whole-Genome Sequencing of Gram-Negative Bacteria Isolated From Bovine Mastitis and Raw Milk: The First Emergence of Colistin mcr-10 and Fosfomycin fosA5 Resistance Genes in Klebsiella pneumoniae in Middle East

Antimicrobial resistance is a major concern in the dairy industry. This study investigated the prevalence, antimicrobial resistance phenotypes, and genome sequencing of Gram-negative bacteria isolated from clinical (n = 350) and subclinical (n = 95) bovine mastitis, and raw unpasteurized milk (n = 125). Klebsiella pneumoniae, Aeromonas hydrophila, Enterobacter cloacae (100% each), Escherichia coli (87.78%), and Proteus mirabilis (69.7%) were the most prevalent multidrug-resistant (MDR) species. Extensive drug-resistance (XDR) phenotype was found in P. mirabilis (30.30%) and E. coli (3.33%) isolates. Ten isolates (four E. coli, three Klebsiella species and three P. mirabilis) that displayed the highest multiple antibiotic resistance (MAR) indices (0.54–0.83), were exposed to whole-genome sequencing (WGS). Two multilocus sequence types (MLST): ST2165 and ST7624 were identified among the sequenced E. coli isolates. Three E. coli isolates (two from clinical mastitis and one from raw milk) belonging to ST2165 showed similar profile of plasmid replicon types: IncFIA, IncFIB, IncFII, and IncQ1 with an exception to an isolate that contained IncR, whereas E. coli ST7624 showed a different plasmid profile including IncHI2, IncHI2A, IncI1α, and IncFII replicon types. ResFinder findings revealed the presence of plasmid-mediated colistin mcr-10 and fosfomycin fosA5 resistance genes in a K. pneumoniae (K1) isolate from bovine milk. Sequence analysis of the reconstructed mcr-10 plasmid from WGS of K1 isolate, showed that mcr-10 gene was bracketed by xerC and insertion sequence IS26 on an IncFIB plasmid. Phylogenetic analysis revealed that K1 isolate existed in a clade including mcr-10-harboring isolates from human and environment with different STs and countries [United Kingdom (ST788), Australia (ST323), Malawi (ST2144), Myanmar (ST705), and Laos (ST2355)]. This study reports the first emergence of K. pneumoniae co-harboring mcr-10 and fosA5 genes from bovine milk in the Middle East, which constitutes a public health threat and heralds the penetration of the last-resort antibiotics. Hence, prudent use of antibiotics in both humans and animals and antimicrobial surveillance plans are urgently required.