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252200.9683Identification and specificity validation of unique and antimicrobial resistance genes to trace suspected pathogenic AMR bacteria and to monitor the development of AMR in non-AMR strains in the environment and clinical settings. The detection of developing antimicrobial resistance (AMR) has become a global issue. The detection of developing antimicrobial resistance has become a global issue. The growing number of AMR bacteria poses a new threat to public health. Therefore, a less laborious and quick confirmatory test becomes important for further investigations into developing AMR in the environment and in clinical settings. This study aims to present a comprehensive analysis and validation of unique and antimicrobial-resistant strains from the WHO priority list of antimicrobial-resistant bacteria and previously reported AMR strains such as Acinetobacter baumannii, Aeromonas spp., Anaeromonas frigoriresistens, Anaeromonas gelatinfytica, Bacillus spp., Campylobacter jejuni subsp. jejuni, Enterococcus faecalis, Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Klebsiella pneumonia subsp. pneumoniae, Pseudomonas aeruginosa, Salmonella enterica subsp. enterica serovar Typhimurium, Thermanaeromonas toyohensis, and Vibrio proteolyticus. Using in-house designed gene-specific primers, 18 different antibiotic resistance genes (algJ, alpB, AQU-1, CEPH-A3, ciaB, CMY-1-MOX-7, CMY-1-MOX-9, CMY-1/MOX, cphA2, cphA5, cphA7, ebpA, ECP_4655, fliC, OXA-51, RfbU, ThiU2, and tolB) from 46 strains were selected and validated. Hence, this study provides insight into the identification of strain-specific, unique antimicrobial resistance genes. Targeted amplification and verification using selected unique marker genes have been reported. Thus, the present detection and validation use a robust method for the entire experiment. Results also highlight the presence of another set of 18 antibiotic-resistant and unique genes (Aqu1, cphA2, cphA3, cphA5, cphA7, cmy1/mox7, cmy1/mox9, asaI, ascV, asoB, oxa-12, acr-2, pepA, uo65, pliI, dr0274, tapY2, and cpeT). Of these sets of genes, 15 were found to be suitable for the detection of pathogenic strains belonging to the genera Aeromonas, Pseudomonas, Helicobacter, Campylobacter, Enterococcus, Klebsiella, Acinetobacter, Salmonella, Haemophilus, and Bacillus. Thus, we have detected and verified sets of unique and antimicrobial resistance genes in bacteria on the WHO Priority List and from published reports on AMR bacteria. This study offers advantages for confirming antimicrobial resistance in all suspected AMR bacteria and monitoring the development of AMR in non-AMR bacteria, in the environment, and in clinical settings.202338058762
260610.9657Pathogenic multiple antimicrobial resistant Escherichia coli serotypes in recreational waters of Mumbai, India: a potential public health risk. Globally, coastal waters have emerged into a pool of antibiotic resistance genes and multiple antibiotic resistant microorganisms, and pathogenicity of these resistant microorganisms in terms of serotypes and virulence genes has made the environment vulnerable. The current study underscores the presence of multiple antibiotic resistant pathogenic serotypes and pathotypes of Escherichia coli, the predominant faecal indicator bacteria (FIB), in surface water and sediment samples of famous recreational beaches (Juhu, Versova, Mahim, Dadar, and Girgaon) of Mumbai. Out of 65 faecal coliforms (FC) randomly selected, 38 isolates were biochemically characterized, serotyped (for 'O' antigen), antibiogram-phenotyped (for 22 antimicrobial agents), and genotyped by polymerase chain reaction (for virulence factors). These isolates belonged to 16 different serotypes (UT, O141, O2, O119, O120, O9, O35, O126, O91, O128, O87, O86, R, O101, O118, and O15) out of which UT (18.4%), O141 (15.7%), and O2 (13.1%) were predominant, indicating its remarkable diversity. Furthermore, the generated antibiogram profile revealed that 95% of these isolates were multiple antibiotic resistant. More than 60% of aminoglycoside-sensitive E. coli isolates exhibited resistance to penicillin, extended penicillin, quinolone, and cephalosporin classes of antibiotic while resistance to other antibiotics was comparatively less. Antibiotic resistance (AR) indexing indicated that these isolates may have rooted from a high-risk source of contamination. Preliminary findings revealed the presence of enterotoxin-encoding genes (stx1 and stx2 specific for enterohaemorrhagic E. coli and Shiga toxin-producing E. coli, heat-stable toxin enterotoxin specific for enterotoxigenic E. coli) in pathogenic serotypes. Thus, government authorities and environmental planners should create public awareness and adopt effective measures for coastal management to prevent serious health risks associated with these contaminated coastal waters.201728316051
523820.9653Snapshot of resistome, virulome and mobilome in aquaculture. Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including bla(TEM-1B), bla(FOX-18), aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.202337604365
562530.9636Genetic characterization and comparative genomics of a multi drug resistant (MDR) Escherichia coli SCM-21 isolated from a subclinical case of bovine mastitis. Escherichia coli is one of the major pathogens causing mastitis that adversely affects the dairy industry worldwide. This study employed whole genome sequence (WGS) approach to characterize the repertoire of antibiotic resistance genes (resistome), virulence genes (virulome), phylogenetic relationship and genome wide comparison of a multi drug resistant (MDR) E. coli(SCM-21) isolated from a case of subclinical bovine mastitis in Bangalore, India. The genome of E. coli SCM- 21 was found to be of 4.29 Mb size with 50.6% GC content, comprising a resistome of 22 genes encoding beta-lactamases (bla(TEM,)bla(AmpC)), polymyxin resistance (arnA) and various efflux pumps (acr, ade, emr,rob, mac, mar, rob), attributing to the bacteria's overall antibiotic resistance genetic profile. The virulome of E. coli SCM-21 consisted of genes encoding different traits [adhesion (ecp, fim, fde), biofilm formation (csg) and toxin production (ent, esp, fep, gsp)], necessary for manifestation of the infection. Phylogenetic relationship of E. coli SCM- 21 with other global E. coli strains (n = 4867) revealed its close genetic relatedness with E. coli strains originating from different hosts of varied geographical regions [human (Germany) bos taurus (USA, Belgium and Scotland) and chicken (China)]. Further, genome wide comparative analysis with E. coli (n = 6) from human and other animal origins showed synteny across the genomes. Overall findings of this study provided a comprehensive insight of the hidden genetic determinants/power of E. coli SCM-21 that might be responsible for manifestation of mastitis and failure of antibiotic treatment. Aforesaid strain forms a reservoir of antibiotic resistance genes (ARGs) and can integrate to one health micro biosphere.202235397469
843940.9632Comparative genomics analysis and virulence-related factors in novel Aliarcobacter faecis and Aliarcobacter lanthieri species identified as potential opportunistic pathogens. BACKGROUND: Emerging pathogenic bacteria are an increasing threat to public health. Two recently described species of the genus Aliarcobacter, A. faecis and A. lanthieri, isolated from human or livestock feces, are closely related to Aliarcobacter zoonotic pathogens (A. cryaerophilus, A. skirrowii, and A. butzleri). In this study, comparative genomics analysis was carried out to examine the virulence-related, including virulence, antibiotic, and toxin (VAT) factors in the reference strains of A. faecis and A. lanthieri that may enable them to become potentially opportunistic zoonotic pathogens. RESULTS: Our results showed that the genomes of the reference strains of both species have flagella genes (flaA, flaB, flgG, flhA, flhB, fliI, fliP, motA and cheY1) as motility and export apparatus, as well as genes encoding the Twin-arginine translocation (Tat) (tatA, tatB and tatC), type II (pulE and pulF) and III (fliF, fliN and ylqH) secretory pathways, allowing them to secrete proteins into the periplasm and host cells. Invasion and immune evasion genes (ciaB, iamA, mviN, pldA, irgA and fur2) are found in both species, while adherence genes (cadF and cj1349) are only found in A. lanthieri. Acid (clpB), heat (clpA and clpB), osmotic (mviN), and low-iron (irgA and fur2) stress resistance genes were observed in both species, although urease genes were not found in them. In addition, arcB, gyrA and gyrB were found in both species, mutations of which may mediate the resistance to quaternary ammonium compounds (QACs). Furthermore, 11 VAT genes including six virulence (cadF, ciaB, irgA, mviN, pldA, and tlyA), two antibiotic resistance [tet(O) and tet(W)] and three cytolethal distending toxin (cdtA, cdtB, and cdtC) genes were validated with the PCR assays. A. lanthieri tested positive for all 11 VAT genes. By contrast, A. faecis showed positive for ten genes except for cdtB because no PCR assay for this gene was available for this species. CONCLUSIONS: The identification of the virulence, antibiotic-resistance, and toxin genes in the genomes of A. faecis and A. lanthieri reference strains through comparative genomics analysis and PCR assays highlighted the potential zoonotic pathogenicity of these two species. However, it is necessary to extend this study to include more clinical and environmental strains to explore inter-species and strain-level genetic variations in virulence-related genes and assess their potential to be opportunistic pathogens for animals and humans.202235761183
523450.9626A Multidrug-Resistant Escherichia coli Caused the Death of the Chinese Soft-Shelled Turtle (Pelodiscus sinensis). The rapid increase in drug resistance in recent years has become a significant global public health concern. Escherichia coli are ubiquitous bacteria, widely distributed in various environments. This study isolated a bacterial strain (HD-593) from diseased Chinese soft-shelled turtles (Pelodiscus sinensis). The bacterium was identified based on morphology, biochemical tests, and 16S rRNA sequencing, confirming it as E. coli. Drug susceptibility tests revealed that the HD-593 strain was highly resistant to ceftriaxone, enrofloxacin, doxycycline, sulfadiazine, gentamicin, neomycin, florfenicol, carbenicillin, cefradine, erythromycin, penicillin, ampicillin, midecamycin, and streptomycin. Resistance gene analysis confirmed the presence of quinolone resistance genes (oqxA and oqxB), aminoglycoside resistance genes (aac(3)-II and aphA1), a β-lactam resistance gene (blaTEM), and an acylaminol resistance gene (floR) in HD-593. The median lethal dose (LD50) of HD-593 for P. sinensis was 6.53 × 10(5) CFU/g. Biochemical analysis of serum revealed that HD-593 infection caused a significant reduction in total protein, albumin, and globulin levels, while markedly increasing the levels of aspartate aminotransferase, alanine aminotransferase, and alkaline phosphatase. Histopathological analysis revealed severe intestinal damage characterized by villi detachment and muscle cell necrosis. Additionally, extensive splenocyte necrosis with nuclear marginalization, glomerular swelling, and pronounced hepatic steatosis accompanied by distended sinusoids were observed. This study identified a multidrug-resistant E. coli strain from deceased P. sinensis, suggesting that drug resistance genes may circulate in aquaculture ecosystems, posing potential risks to aquaculture.202540431566
139360.9625Prevalence, antimicrobial resistance and detection of virulence genes of Escherichia coli and Salmonella spp. isolated from white-lipped peccaries and collared peccaries. Salmonella spp. and Escherichia coli are implicated in human and animal infections and require antimicrobial treatment in many situations. Faecal samples of healthy white-lipped peccaries (Pecari tajacu) (n = 30) and collared peccaries (Tayassu pecari ) (n = 60) obtained in three farms located in the Midwest Brazil. The antimicrobial profiles of commensal E. coli from P. tajacu and T. pecari from commercial herds in Brazil were isolated and analyzed and virulence genes were detected. Among 90 healthy animals, no Salmonella spp. were isolated. However, 30 samples (27%) tested positive for E. coli, with 18 isolates from P. tajacu and 12 from T. pecari, representing frequencies of 58.0% and 38.7%, respectively. Additionally, other Enterobacteriaceae family bacteria were detected but not included in this analysis. However, individual samples from 30 animals tested positive for E. coli, of which 16 were isolated from P. tajacu presenting multidrug resistance and six were isolated from T. pecari presenting a similar pattern. The E. coli virulence genes detected were papC (pilus-associated pyelonephritis) in five isolates, tsh (temperature-sensitive hemagglutinin) in one isolate, and eae (enteric attachment and effacement) in one isolate. The serum resistance gene, iss (increased serum survival), was detected in four isolates. An association between these genes and the presence of hemolysin was also observed in one isolate. Thus, T. pecari and P. tajacu are potential reservoirs of pathogenic and multidrug-resistant and E. coli. Faecal E. coli of healthy P. tajacu and T. pecari could act as a possible reservoir of antimicrobial resistance genes in environment.202438713279
248270.9624Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps. Prophages affect bacterial fitness on multiple levels. These include bacterial infectivity, toxin secretion, virulence regulation, surface modification, immune stimulation and evasion and microbiome competition. Lysogenic conversion arms bacteria with novel accessory functions thereby increasing bacterial fitness, host adaptation and persistence, and antibiotic resistance. These properties allow the bacteria to occupy a niche long term and can contribute to chronic infections and inflammation such as chronic rhinosinusitis (CRS). In this study, we aimed to identify and characterize prophages present in Staphylococcus aureus from patients suffering from CRS in relation to CRS disease phenotype and severity. Prophage regions were identified using PHASTER. Various in silico tools like ResFinder and VF Analyzer were used to detect virulence genes and antibiotic resistance genes respectively. Progressive MAUVE and maximum likelihood were used for multiple sequence alignment and phylogenetics of prophages respectively. Disease severity of CRS patients was measured using computed tomography Lund-Mackay scores. Fifty-eight S. aureus clinical isolates (CIs) were obtained from 28 CRS patients without nasal polyp (CRSsNP) and 30 CRS patients with nasal polyp (CRSwNP). All CIs carried at least one prophage (average=3.6) and prophages contributed up to 7.7 % of the bacterial genome. Phage integrase genes were found in 55/58 (~95 %) S. aureus strains and 97/211 (~46 %) prophages. Prophages belonging to Sa3int integrase group (phiNM3, JS01, phiN315) (39/97, 40%) and Sa2int (phi2958PVL) (14/97, 14%) were the most prevalent prophages and harboured multiple virulence genes such as sak, scn, chp, lukE/D, sea. Intact prophages were more frequently identified in CRSwNP than in CRSsNP (P=0.0021). Intact prophages belonging to the Sa3int group were more frequent in CRSwNP than in CRSsNP (P=0.0008) and intact phiNM3 were exclusively found in CRSwNP patients (P=0.007). Our results expand the knowledge of prophages in S. aureus isolated from CRS patients and their possible role in disease development. These findings provide a platform for future investigations into potential tripartite associations between bacteria-prophage-human immune system, S. aureus evolution and CRS disease pathophysiology.202134907894
121280.9622Virulence Factors and Antimicrobial Resistance of Uropathogenic Escherichia coli EQ101 UPEC Isolated from UTI Patient in Quetta, Balochistan, Pakistan. Infectious diseases have been tremendously increasing as the organisms of even normal flora become opportunistic and cause an infection, and Escherichia coli (E. coli EQ101) is one of them. Urinary tract infections are caused by various microorganisms, but Escherichia coli is the primary cause of almost 70%-90% of all UTIs. It has multiple strains, possessing diverse virulence factors, contributing to its pathogenicity. Furthermore, these virulent strains also can cause overlapping pathogenesis by sharing resistance and virulence factors among each other. The current study is aimed at analyzing the genetic variants associated with multi-drug-resistant (MDR) E. coli using the whole genome sequencing platform. The study includes 100 uropathogenic Escherichia coli (UPEC) microorganisms obtained from urine samples out of which 44% were multi-drug-resistant (MDR) E. coli. Bacteria have been isolated and antimicrobial susceptibility test (AST) was determined by disk diffusion method on the Mueller-Hinton agar plate as recommended by the Clinical and Laboratory Standards Institute (CLSI) 2020, and one isolate has been selected which shows resistance to most of the antibiotics, and that isolate has been analyzed by whole genome sequencing (WGS), accompanied by data and phylogenetic analysis, respectively. Organisms were showing resistance against ampicillin (10 μg), cefixime (5 μg), ceftriaxone (30 μg), nalidixic acid (30 μg), ciprofloxacin (5 μg), and ofloxacin (5 μg) on antimicrobial susceptibility test. WGS were done on selected isolate which identified 25 virulence genes (air, astA, chuA, fyuA, gad, hra, iha, irp2, iss, iucC, iutA, kpsE, kpsMII_K1, lpfA, mchF, ompT, papA_F43, sat, senB, sitA, terC, traT, usp, vat, and yfcV) and seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA). Among resistance genes, seven genes (TolC, emrR, evgA, qacEdelta1, H-NS, cpxA, and mdtM) were identified to be involved in antibiotic efflux, three AMR genes (aadA5, mphA, and CTX-M-15) were involved in antibiotic inactivation, and two genes (sul1 and dfrA14) were found to be involved in antibiotic drug replacement. Our data identified antibiotic resistance and virulence genes of the isolate. We suggest further research work to establish region-based resistance profile in comparison with the global resistance pattern.202337727279
134790.9622Microbiological quality and antimicrobial resistance characterization of Salmonella spp. in fresh milk value chains in Ghana. Consumer perception of poor hygiene of fresh milk products is a major barrier to promotion of milk consumption as an intervention to alleviate the burden of malnutrition in Ghana. Fresh milk is retailed raw, boiled, or processed into unfermented cheese and spontaneously fermented products in unlicensed outlets. In this study, we have determined microbiological quality of informally retailed fresh milk products and characterized the genomic diversity and antimicrobial resistance (AMR) patterns of non-typhoidal Salmonella (NTS) in implicated products. A total of 159 common dairy products were purchased from five traditional milk markets in Accra. Samples were analysed for concentrations of aerobic bacteria, total and fecal coliforms, Escherichia coli, staphylococci, lactic acid bacteria and yeast and moulds. The presence of Salmonella, E. coli O157:H7, Listeria monocytogenes and Staphylococcus aureus were determined. AMR of Salmonella against 18 antibiotics was experimentally determined. Genome sequencing of 19 Salmonella isolates allowed determination of serovars, antigenic profiles, prediction of AMR genes in silico and inference of phylogenetic relatedness between strains. Raw and heat-treated milk did not differ significantly in overall bacterial quality (P = 0.851). E. coli O157:H7 and Staphylococcus aureus were present in 34.3% and 12.9% of dairy products respectively. Multidrug resistant (MDR) Salmonella enterica serovars Muenster and Legon were identified in 11.8% and 5.9% of unfermented cheese samples respectively. Pan genome analysis revealed a total of 3712 core genes. All Salmonella strains were resistant to Trimethoprim/Sulfamethoxazole, Cefoxitin, Cefuroxime Axetil and Cefuroxime. Resistance to Chloramphenicol (18%) and Ciprofloxacin (100%), which are first line antibiotics used in treatment of NTS bacteremia in Ghana, was evident. AMR was attributed to presence and/or mutations in the following genes: golS, sdiA for cephalosporins, aac(6')-Iy, ant(9) for aminoglycosides, mdtK, gyrA, gyrB, parC, parE for quinolones and cat1, cat4 for phenicols. Phylogenetic analysis based on accessory genes clustered S. Legon strains separately from the S. Muenster strains. These strains were from different markets suggesting local circulation of related strains. Our study justifies consumer resistance to consumption of unripened soft cheese without further lethal heat treatment, and provides evidence that supports the Ghana Health Service recommendation for use of 3rd generation cephalosporins for the treatment of MDR NTS infections.201829680695
2782100.9622Urban dust fecal pollution in Mexico City: antibiotic resistance and virulence factors of Escherichia coli. Fecal pollution of settled dust samples from indoor and outdoor urban environments, was measured and characterized by the presence of fecal coliforms (FC), and by the characterization of Escherichia coli virulence genes, adherence and antibiotic resistance traits as markers. There were more FC indoors than outdoors (mean values 1089 and 435MPN/g). Among indoor samples, there were more FC in houses with carpets and/or pets. Using a PCR-based assay for six enteropathogenicity genes (belonging to the EAEC, EHEC and EPEC pathotypes) on randomly selected E. coli isolates, there was no significant difference between isolates from indoors and outdoors (60% and 72% positive to at least one gene). The serotypes commonly associated with pathogenic strains, such as O86 and O28, were found in the indoor isolates; whereas O4, O66 and O9 were found amongst outdoor isolates. However, there were significantly more outdoor isolates resistant to at least one antibiotic (73% vs. 45% from indoors) among the strains positive for virulence factors, and outdoor isolates were more commonly multiresistant. There was no relationship between the presence of virulence genes and resistance traits. These results indicate that outdoor fecal bacteria were more likely from human sources, and those found indoors were related to pets and maintained in carpets. This study illustrates the risk posed by fecal bacteria from human sources, usually bearing virulence and resistance traits. Furthermore, the high prevalence of strains carrying genes associated to EAEC or EHEC pathotypes, in both indoor and outdoor environments, adds to the health risk.200616762593
6045110.9621Lacticaseicin 30 and Colistin as a Promising Antibiotic Formulation against Gram-Negative β-Lactamase-Producing Strains and Colistin-Resistant Strains. Antimicrobial resistance is a global health concern across the world and it is foreseen to swell if no actions are taken now. To help curbing this well announced crisis different strategies are announced, and these include the use of antimicrobial peptides (AMP), which are remarkable molecules known for their killing activities towards pathogenic bacteria. Bacteriocins are ribosomally synthesized AMP produced by almost all prokaryotic lineages. Bacteriocins, unlike antibiotics, offer a set of advantages in terms of cytotoxicity towards eukaryotic cells, their mode of action, cross-resistance and impact of microbiota content. Most known bacteriocins are produced by Gram-positive bacteria, and specifically by lactic acid bacteria (LAB). LAB-bacteriocins were steadily reported and characterized for their activity against genetically related Gram-positive bacteria, and seldom against Gram-negative bacteria. The aim of this study is to show that lacticaseicin 30, which is one of the bacteriocins produced by Lacticaseibacillus paracasei CNCM I-5369, is active against Gram-negative clinical strains (Salmonella enterica Enteritidis H10, S. enterica Typhimurium H97, Enterobacter cloacae H51, Escherichia coli H45, E. coli H51, E. coli H66, Klebsiella oxytoca H40, K. pneumoniae H71, K. variicola H77, K. pneumoniae H79, K. pneumoniae H79), whereas antibiotics failed. In addition, lacticaseicin 30 and colistin enabled synergistic interactions towards the aforementioned target Gram-negative clinical strains. Further, the combinations of lacticaseicin 30 and colistin prompted a drastic downregulation of mcr-1 and mcr-9 genes, which are associated with the colistin resistance phenotypes of these clinical strains. This report shows that lacticaseicin 30 is active against Gram-negative clinical strains carrying a rainbow of mcr genes, and the combination of these antimicrobials constitutes a promising therapeutic option that needs to be further exploited.202135052897
5451120.9621Two novel phages, Klebsiella phage GADU21 and Escherichia phage GADU22, from the urine samples of patients with urinary tract infection. Phages are found in a wide variety of places where bacteria exist including body fluids. The aim of the present study was to isolate phages from the urine samples of patients with urinary tract infection. The 10 urine samples were cultured to isolate bacteria and also used as phage sources against the isolated bacteria. From 10 urine samples with positive cultures, 3 phages were isolated (33%) and two of them were further studied. The Klebsiella phage GADU21 and Escherichia phage GADU22 phages infected Klebsiella pneumonia and Escherichia coli, respectively. Among the tested 14 species for host range analysis, the Klebsiella phage GADU21 was able to infect two species which are Klebsiella pneumonia and Proteus mirabilis, and Escherichia phage GADU22 was able to infect four species which are Shigella flexneri, Shigella sonnei and Escherichia coli. Among different isolates of the indicator bacteria for each phage, GADU21 infected half of the tested 20 Klebsiella pneumonia isolates while GADU22 infected 85% of the tested 20 E. coli isolates. The genome sizes and GC ratios were 75,968 bp and 44.4%, and 168,023 bp and 35.3% for GADU21 and GADU22, respectively. GADU21 and GADU22 were both lytic and had no antibiotic resistance and virulence genes. GADU21 was homologue with Klebsiella phage vB_KpP_FBKp27 but only 88% of the genome was covered by this phage. The non-covered parts of the GADU21 genome included genes for tail-fiber-proteins and HNH-endonuclease. GADU22 had 94.8% homology with Escherichia phage vB_Eco_OMNI12 and had genes for immunity proteins. Phylogenetic analysis showed GADU21 and GADU22 were members of Schitoviridae family and Efbeekayvirus genus and Straboviridae family and Tevenvirinae genus, respectively. VIRIDIC analysis classified these phages in new species clusters. Our study demonstrated the possibility to use infected body fluids as phage sources to isolate novel phages. GADU21 is the first reported Klebsiella phage isolated from human body fluid. The absence of virulence and antibiotic resistance genes in their genomes makes the phages a potential therapeutic tool against infections.202438238612
1210130.9620Detection of numerous verotoxigenic E. coli serotypes, with multiple antibiotic resistance from cattle faeces and soil. Verotoxigenic E. coli (VTEC) belong to a diverse range of serotypes. Serotypes O157 and O26 are predominately identified in VTEC-associated disease in Europe, however due to difficulty in detection little is known about the epidemiology of non-O157 serotypes. This study reports the identification of 7 VTEC serotypes from cattle faeces and soil. Cattle faeces samples (n=128) were taken from animals in 6 different farms, with soil samples (n=20) obtained from 1 farm. After sample incubation in modified tryptone soy broth (mTSB) supplemented with streptomycin sulphate samples were plated onto sorbitol MacConkey (SMAC) also supplemented with streptomycin sulphate. Bacteria detected on the plates were subjected to biochemical testing, antibiotic resistance profiling, and PCR to detect typical virulence genes, beta-lactamase and class 1 integron associated genes. Serotyping was performed on isolates positive for virulence genes. E. coli was identified from 103 samples, with verotoxin genes present in 7 E. coli isolates. Of these 7 isolates, 5 were resistant to 5 or more antibiotics. The isolate resistant to 9 antimicrobials contained a class 1 integron structure. Serotyping identified 7 separate VTEC, O2:H27, O26:H11, O63:H(-), O148:H8, O149:H1, O174:H21 and ONT:H25. Six of these VTEC have been previously associated with human disease, however with the exception of O26:H11, these serotypes have been rarely reported worldwide. Increased surveillance is required to determine the prevalence of these and other non-O157 VTEC. The presence of multi-antibiotic resistance in these isolates is of concern, and the overall implications for public health must be ascertained.200918838234
2524140.9620Phenotypic and Genotype Patterns of Antimicrobial Resistance in Non-Human Primates: An Overlooked "One Health" Concern. Non-human primates (NHPs) are close relatives of humans and can serve as hosts for many zoonotic pathogens. They play crucial role in spreading antimicrobial resistant bacteria (AMR) to humans across various ecological niches. The spread of antimicrobial resistance in NHPs may complicate wildlife conservation efforts, as it may threaten domestic livestock, endangered species as well as human's health. This review analyses the existing literature on the prevalence of AMR in NHP species, including Rhinopithecus roxellana, Macaca fascicularis, and Sapajus nigritus, to create awareness in all stake holders involve in the fight against AMR on the serious potential threats that these primates pose. METHODS: We performed a comprehensive literature search using the PubMed (National Library of Medicine-NLM), Scopus (Elsevier), Web of Science Core Collection (Clarivate Analytics), Springer Link (Springer), and Science Direct (Elsevier) databases until January, 2025. The search strategy combined terms from the areas of non-human primates, antibiotic resistance, antimicrobial resistance, and antibacterial resistance genes (ARGs). Studies that isolated bacteria from NHPs and assessed phenotypic resistance to specific antibiotics as well as studies that identified ARGs in bacteria isolated from NHPs were included. Data were synthesised thematically across all included studies. RESULTS: A total of 37 studies were included (explained as Cercopithecidae (n = 23), Callithrix (n = 6), Cebidae (n = 4), Hominidae (n = 3), and Atelidae (n = 1)). The results showed that the most common ARB across the various NHPs and geographical settings was Staphylococcus spp. (45.95%) and Escherichia spp. (29.73%). The tested antibiotics that showed high levels of resistance in NHPs included Tetracycline (40.54%), Ciprofloxacin (32.43%), and Erythromycin (24.34%), whereas ermC, tetA, tetM, aadA, aph (3″)-II, and qnrS1 were the most widely distributed antibiotic resistance genes in the studies. CONCLUSION: NHPs are potential natural reservoirs of AMR, therefore global policy makers should consider making NHPs an indicator species for monitoring the spread of ARB.202541148677
5239150.9619The mobile gene cassette carrying tetracycline resistance genes in Aeromonas veronii strain Ah5S-24 isolated from catfish pond sediments shows similarity with a cassette found in other environmental and foodborne bacteria. Aeromonas veronii is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen that causes diarrhea in humans and hemorrhagic septicemia in fish. In the present study, we used whole-genome sequencing (WGS) to evaluate the presence of antimicrobial resistance (AMR) and virulence genes found in A. veronii Ah5S-24 isolated from catfish pond sediments in South-East, United States. We found cphA4, dfrA3, mcr-7.1, valF, bla (FOX-7), and bla (OXA-12) resistance genes encoded in the chromosome of A. veronii Ah5S-24. We also found the tetracycline tet(E) and tetR genes placed next to the IS5/IS1182 transposase, integrase, and hypothetical proteins that formed as a genetic structure or transposon designated as IS5/IS1182/hp/tet(E)/tetR/hp. BLAST analysis showed that a similar mobile gene cassette (MGC) existed in chromosomes of other bacteria species such as Vibrio parahaemolyticus isolated from retail fish at markets, Aeromonas caviae from human stool and Aeromonas media from a sewage bioreactor. In addition, the IS5/IS1182/hp/tet(E)/tetR/hp cassette was also found in the plasmid of Vibrio alginolyticus isolated from shrimp. As for virulence genes, we found the tap type IV pili (tapA and tapY), polar flagellae (flgA and flgN), lateral flagellae (ifgA and IfgL), and fimbriae (pefC and pefD) genes responsible for motility and adherence. We also found the hemolysin genes (hylII, hylA, and TSH), aerA toxin, biofilm formation, and quorum sensing (LuxS, mshA, and mshQ) genes. However, there were no MGCs encoding virulence genes found in A. veronii AhS5-24. Thus, our findings show that MGCs could play a vital role in the spread of AMR genes between chromosomes and plasmids among bacteria in aquatic environments. Overall, our findings are suggesting that MGCs encoding AMR genes could play a vital role in the spread of resistance acquired from high usage of antimicrobials in aquaculture to animals and humans.202337007502
2099160.9619Antibiotic-resistant bacteria and resistance-genes in drinking water source in north Shoa zone, Amhara region, Ethiopia. BACKGROUND: The growing number of antimicrobial-resistant bacteria in a range of environments poses a serious challenge to infectious disease prevention. Good water quality is critical to human health and has a direct impact on a country's socio-economic growth. Therefore, assessing the bacteriological quality of drinking water provides benchmark data and provides insight into the development of further protection and treatment measures. METHODS: A cross-sectional study was conducted from February 1, 2022, to September 31, 2023, in the diarrhea hotspot areas of North Shewa Zone (Minjar-Shenkora and Mojana-Wedera districts). Water samples were collected from drinking water sources (hand-pumps, boreholes, wells, spring water and ponds) to assess the quality following WHO guidelines. The collected water samples were processed for bacterial isolation, antimicrobial susceptibility testing, and detection of antimicrobial resistance genes. Data were entered and analyzed using the Statistical Package for the Social Sciences (SPSS) version 25. RESULTS: A total of (49/138, 35.5%) bacteria were isolated from 138 drinking water samples, with a positive rate of (41/138, 29.7%). Among the isolates, (16/138, 11.6%) were Staphylococcus aureus while (33/138, 23.9%) were members of Enterobacteriaceae. Relatively high resistance rate among all isolates were observed for the most prescribed antibiotics in Ethiopia, including erythromycin, cotrimoxazole, doxycycline, ceftriaxone, gentamicin, and chloramphenicol. However, a low resistance was observed for early introduced antibiotics such as ciprofloxacin and recently introduced antibiotics such as cefotaxime, ceftazidime, imipenem, and meropenem. Among the 49 bacteria isolates, (32/49, 65.3%) were multidrug-resistant (MDR) pathogens while (12/49, 24.5%) were ESβL producers. Different ESβL genes were detected in most bacterial isolates. The predominant ESβL genes were blaCTX-M-gp8/25 (6/33, 18.2%), blaCTX-M-gp9 (5/33, 15.2%), and blaCTX-M-gp1 (5/33, 15.2%). CONCLUSION: The result of this study suggests that most water sources in the study area were contaminated by various bacterial species that are resistant to different antibiotics. Various ESβL resistance genes have also been detected. Therefore, regular sanitary inspection and bacteriological analysis should be mandatory to protect drinking water sources from contamination and the persistence of resistant bacteria.202439310913
942170.9619Occurrence of multidrug resistant Gram-negative bacteria and resistance genes in semi-aquatic wildlife - Trachemys scripta, Neovison vison and Lutra lutra - as sentinels of environmental health. Emergence of antimicrobial resistance (AMR) in bacterial pathogens has been recognized as a major public health concern worldwide. In the present study, antimicrobial resistant Gram-negative bacteria (AMRGNB) and AMR genes were assessed in semi-aquatic wild animals from a highly populated and intensive farming region of Spain, Catalonia. Cloacal/rectal swab samples were collected from 241 animals coming from invasive species Trachemys scripta (n = 91) and Neovison vison (n = 131), and endangered-protected species Lutra lutra (n = 19). Accordingly, 133 (55.2%) isolates were identified as AMRGNB. Escherichia coli and Pseudomonas fluorescens were among the bacteria most frequently isolated in all animal species, but other nosocomial agents such as Klebsiella pneumoniae, Salmonella spp. or Citrobacter freundii, were also prevalent. The phenotypic susceptibility testing showed the highest resistance to β-lactams (91%). Molecular analysis showed 25.3% of turtles (15.4% ESBL/Ampc genes), 21% of Eurasian otters (10.5% ESBL/Ampc genes) and 14.5% of American minks (8.4% ESBL/Ampc genes) were positive to AMR genes. The genotyping frequency was tetM (20.6%), blaCMY-2 (13%), ermB (6.1%), blaCMY-1 (4.6%), blaCTX-M-15 (3.1%) and mcr-4 (0.8%). Turtles had a larger prevalence of AMRGNB and AMR genes than mustelids, but American mink carried mcr-4 colistin-resistance gene. Moreover, cluster analysis of AMR gene distribution revealed that an ESBL/AmpC cluster in a highly populated area comprising big metropolitan regions, and another tetM/emrB cluster in an expended area with highly intensive livestock production. Although the mcr-4 positive case was not included in those clusters, that case was found in a county with a high pig farm density. In conclusion, semi-aquatic wild animals are a good sentinel for environmental contamination with AMRGNB and AMR genes. Therefore, One Health Approach is urgently needed in highly populated regions, and with intensive livestock production like Catalonia.202235341839
1655180.9618Genomic analysis of Escherichia coli circulating in the Brazilian poultry sector. Escherichia coli are gut commensal bacteria and opportunistic pathogens, and the emergence of antimicrobial resistance threatens the safety of the food chain. To know the E. coli strains circulating in the Brazilian poultry sector is important since the country corresponds to a significant chicken meat production. Thus, we analyzed 90 publicly genomes available in a database using web-based tools. Genomic analysis revealed that sul alleles were the most detected resistance genes, followed by aadA, bla(CTX-M), and dfrA. Plasmids of the IncF family were important, followed by IncI1-Iα, Col-like, and p0111. Genes of specific metabolic pathways that contribute to virulence (terC and gad) were predominant, followed by sitA, traT, and iss. Additionally, pap, usp, vat, sfa/foc, ibeA, cnf1, eae, and sat were also predicted. In this regard, 11 E. coli were characterized as avian pathogenic E. coli and one as atypical enteropathogenic E. coli. Phylogenetic analysis confirmed the predominant occurrence of B1 but also A, D, B2, F, E, G, C, and Clade I phylogroups, whereas international clones ST38, ST73, ST117, ST155, and ST224 were predicted among 53 different sequence types identified. Serotypes O6:H1 and:H25 were prevalent, and fimH31 and fimH32 were the most representatives among the 36 FimH types detected. Finally, single nucleotide polymorphisms-based phylogenetic analysis confirmed high genomic diversity among E. coli strains. While international E. coli clones have adapted to the Brazilian poultry sector, the virulome background of these strains support a pathogenic potential to humans and animals, with lineages carrying resistance genes that can lead to hard-to-treat infections.202235864380
1388190.9618Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy. Animals, humans and food are all interconnected sources of antimicrobial resistance (AMR), allowing extensive and rapid exchange of AMR bacteria and genes. Whole genome sequencing (WGS) was used to characterize 279 Escherichia coli isolates obtained from animals (livestock, companion animals, wildlife), food and humans in Italy. E. coli predominantly belonged to commensal phylogroups B1 (46.6%) and A (29%) using the original Clermont criteria. One hundred and thirty-six sequence types (STs) were observed, including different pandemic (ST69, ST95, ST131) and emerging (ST10, ST23, ST58, ST117, ST405, ST648) extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Eight antimicrobial resistance genes (ARGs) and five chromosomal mutations conferring resistance to highest priority critically important antimicrobials (HP-CIAs) were identified (qnrS1, qnrB19, mcr-1, bla(CTX-M1,15,55), bla(CMY-2), gyrA/parC/parE, ampC and pmrB). Twenty-two class 1 integron arrangements in 34 strains were characterized and 11 ARGs were designated as intI1 related gene cassettes (aadA1, aadA2, aadA5, aad23, ant2_Ia, dfrA1, dfrA7, dfrA14, dfrA12, dfrA17, cmlA1). Notably, most intI1 positive strains belonged to rabbit (38%) and poultry (24%) sources. Three rabbit samples carried the mcr-1 colistin resistance gene in association with IS6 family insertion elements. Poultry meat harbored some of the most prominent ExPEC STs, including ST131, ST69, ST10, ST23, and ST117. Wildlife showed a high average number of virulence-associated genes (VAGs) (mean = 10), mostly associated with an ExPEC pathotype and some predominant ExPEC lineages (ST23, ST117, ST648) were identified.202033172096