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764600.9591Assessment of Bacterial Community and Other Microorganism Along the Lam Takhong Watercourse, Nakhon Ratchasima, Thailand. Lam Takhong, a vital watercourse in Nakhon Ratchasima province, Thailand, supports agricultural, recreational, and urban activities. Originating in a national park, it flows through urban areas before discharging into a dam and running off via the sluice gate. While water quality monitoring is routine, microbial community data have never been reported. This study assesses the microorganism diversity and functional genes in Lam Takhong watercourse using a shotgun sequencing metagenomics approach. Water samples were collected from the upstream, midstream, and downstream sections. The midstream area exhibited the highest abundance of fecal coliform bacteria, plankton, and benthos, suggesting elevated pollution levels. Genes related to metabolism, particularly carbohydrate and amino acid pathways, were predominant. Proteobacteria was the most abundant phylum found in the water, with Limnohabitans as the dominant planktonic bacteria. Bacteria such as Staphylococcus, Mycobacterium, Escherichia, Pseudomonas, Enterococcus, Neisseria, Streptomyces, and Salmonella were detected, along with antibiotic resistance genes, raising public health concerns. These findings emphasize the need for microbial monitoring in the Lam Takhong to determine the potential water quality bioindicator and prevent potential disease spread through the water system.202540244481
234310.9587Investigation of Virulence Genes of the Predominant Bacteria Associated with Renal Stones and their Correlation with Postoperative Septic Complications. PURPOSE: Nephrolithiasis is a worldwide disease, and 4.7% of the patients may develop postoperative sepsis. Characterization of virulence genes of bacteria associated with renal stones is still lacking in the literature. The study aimed to investigate the virulence genes of the predominant stone bacterial isolate and their association with postoperative septic complications in patients treated with percutaneous nephrolithotomy (PCNL). METHODS: Stone and midstream urine samples were collected from 200 nephrolithiasis patients who underwent PCNL. Microbiological examination and virulence profile were studied for the common bacteria isolated from the stones. RESULTS: Microbiological analysis revealed that Staphylococcus aureus was the predominant organism in stone samples (42.8%), while Escherichia coli (56.6%) was the dominant pathogen in midstream urine. Eight patients (4%) developed septic complications; stone culture was positive for S. aureus in seven and E. coli in one patient, while all but one had negative midstream urine. The patient with positive midstream urine culture had also S. aureus infection. Detection of virulence genes in S. aureus isolated from stones showed a high positivity of the hemolysine gene hla (93.3%) and adhesion gene fnbA (73.3%), whereas enterotoxin genes (sec and sea) were negative in all S. aureus stone cultures. Moreover, the adhesion genes (fnbB and can), hemolysine gene (hlb), panton-valentine leukocidin (pvl) gene and the enterotoxin gene (seb) were significantly higher in septic patients compared to the non-septic ones (p< 0.05). Interestingly, there was a significant relation between the existence of virulence genes and the resistance of antibiotics (p < 0.05). CONCLUSION: There has been a notable shift toward gram-positive organisms (S. aureus) in the stone culture. Moreover, S. aureus virulence genes were significantly attributed to the resistance of some antibiotics and postoperative septic complications, suggesting that the stone culture could be more informative than urine culture, especially in predicting the risk of postoperative sepsis.202235844358
524520.9581Antimicrobial Resistance in U.S. Retail Ground Beef with and without Label Claims Regarding Antibiotic Use. ABSTRACT: Antibiotics used during food animal production account for approximately 77% of U.S. antimicrobial consumption by mass. Ground beef products labeled as raised without antibiotics (RWA) are perceived to harbor lower levels of antimicrobial-resistant bacteria than conventional (CONV) products with no label claims regarding antimicrobial use. Retail ground beef samples were obtained from six U.S. cities. Samples with an RWA or U.S. Department of Agriculture Organic claim (n = 299) were assigned to the RWA production system. Samples lacking these claims (n = 300) were assigned to the CONV production system. Each sample was cultured for the detection of five antimicrobial-resistant bacteria. Genomic DNA was isolated from each sample, and a quantitative PCR assay was used to determine the abundance of 10 antimicrobial resistance (AMR) genes. Prevalence of tetracycline-resistant Escherichia coli (CONV, 46.3%; RWA, 34.4%; P < 0.01) and erythromycin-resistant Enterococcus (CONV, 48.0%; RWA, 37.5%; P = 0.01) was higher in CONV ground beef. Salmonella was detected in 1.2% of samples. The AMR gene blaCTX-M (CONV, 4.1 log-normalized abundance; RWA, 3.8 log-normalized abundance; P < 0.01) was more abundant in CONV ground beef. The AMR genes mecA (CONV, 4.4 log-normalized abundance; RWA, 4.9 log-normalized abundance; P = 0.05), tet(A) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), tet(B) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), and tet(M) (CONV, 5.4 log-normalized abundance; RWA, 5.8 log-normalized abundance; P < 0.01) were more abundant in RWA ground beef. Although these results suggest that antimicrobial use during U.S. cattle production does not increase human exposure to antimicrobial-resistant bacteria via ground beef, quantitative microbiological risk assessments are required for authoritative determination of the human health impacts of the use of antimicrobial agents during beef production.202133302298
125330.9580Phenotypic and Genotypic Assessment of Antibiotic Resistance and Genotyping of vacA, cagA, iceA, oipA, cagE, and babA2 Alleles of Helicobacter pylori Bacteria Isolated from Raw Meat. BACKGROUND: Foodstuffs with animal origins, particularly meat, are likely reservoirs of Helicobacter pylori. PURPOSE: An existing survey was accompanied to assess phenotypic and genotypic profiles of antibiotic resistance and genotyping of vacA, cagA, cagE, iceA, oipA, and babA2 alleles amongst the H. pylori bacteria recovered from raw meat. METHODS: Six-hundred raw meat samples were collected and cultured. H. pylori isolates were tested using disk diffusion and PCR identification of antibiotic resistance genes and genotyping. RESULTS: Fifty-two out of 600 (8.66%) raw meat samples were contaminated with H. pylori. Raw ovine meat (13.07%) had the uppermost contamination. H. pylori bacteria displayed the uppermost incidence of resistance toward tetracycline (82.69%), erythromycin (80.76%), trimethoprim (65.38%), levofloxacin (63.46%), and amoxicillin (63.46%). All H. pylori bacteria had at least resistance toward one antibiotic, even though incidence of resistance toward more than eight antibiotics was 28.84%. Total distribution of rdxA, pbp1A, gyrA, and cla antibiotic resistance genes were 59.61%, 51.92%, 69.23%, and 65.38%, respectively. VacA s1a (84.61%), s2 (76.92%), m1a (50%), m2 (39.13%), iceA1 (38.46%), and cagA (55.76%) were the most generally perceived alleles. S1am1a (63.46%), s2m1a (53.84%), s1am2 (51.92%), and s2m2 (42.30%) were the most generally perceived genotyping patterns. Frequency of cagA-, oipA-, and babA2- genotypes were 44.23%, 73.07%, and 80.76%, respectively. A total of 196 combined genotyping patterns were also perceived. CONCLUSION: The role of raw meat, particularly ovine meat, in transmission of virulent and resistant H. pylori bacteria was determined. VacA and cagA genotypes had the higher incidence. CagE-, babA2-, and oipA- H. pylori bacteria had the higher distribution. Supplementary surveys are compulsory to originate momentous relations between distribution of genotypes, antibiotic resistance, and antibiotic resistance genes.202032099418
122340.9570Characterization of Escherichia coli virulence genes, pathotypes and antibiotic resistance properties in diarrheic calves in Iran. BACKGROUND: Calf diarrhea is a major economic concern in bovine industry all around the world. This study was carried out in order to investigate distribution of virulence genes, pathotypes, serogroups and antibiotic resistance properties of Escherichia coli isolated from diarrheic calves. RESULTS: Totally, 76.45% of 824 diarrheic fecal samples collected from Isfahan, Chaharmahal, Fars and Khuzestan provinces, Iran were positive for E. coli and all of them were also positive for cnf2, hlyA, cdtIII, f17c, lt, st, stx1, eae, ehly, stx2 and cnf1 virulence genes. Chaharmahal had the highest prevalence of STEC (84.61%), while Isfahan had the lowest (71.95%). E. coli serogroups had the highest frequency in 1-7 days old calves and winter season. Distribution of ETEC, EHEC, AEEC and NTEC pathotypes among E. coli isolates were 28.41%, 5.07%, 29.52% and 3.49%, respectively. Statistical analyses were significant for presence of bacteria between various seasons and ages. All isolates had the high resistance to penicillin (100%), streptomycin (98.25%) and tetracycline (98.09%) antibiotics. The most commonly detected resistance genes were aadA1, sul1, aac[3]-IV, CITM, and dfrA1. The most prevalent serogroup among STEC was O26. CONCLUSIONS: Our findings should raise awareness about antibiotic resistance in diarrheic calves in Iran. Clinicians should exercise caution when prescribing antibiotics.201425052999
218650.9568Bacterial drug-resistance patterns and genetic diversity of bacteria-associated bacteriuria in diabetic patients in Ghana. OBJECTIVES: Our study aimed to determine the etiology of urinary tract infections (UTIs), resistance profiles of isolated bacteria, and virulence factors of Escherichia coli associated with bacteriuria in diabetic patients in Ghana. METHODS: Midstream urine samples from 982 diabetic patients were tested for uropathogens at the National Diabetes Management and Research Centre in Ghana, using standard bacteriological methods, with antibiogram testing of the isolates using the Kirby-Bauer disk diffusion, as per CLSI guidelines. Polymerase chain reaction (PCR) was used to investigate the phylogenetic groupings and virulence factor (VF) genes of isolated E. coli. RESULTS: The overall prevalence of UTIs was 9.2%, and the main uropathogens were Klebsiella spp. (55.6%) and Escherichia coli (31.3%). Age, duration of diabetes, and a previous history of UTIs were risk factors associated with UTI (p-value < 0.05). High levels of antibacterial resistance to cefuroxime (84%), ampicillin (80%), and gentamicin (70.7%) were observed. The distribution of VFs in each phylogenetic group revealed that sfa-iutA-KpsTMII-KpsTMIII genes were associated with group B2, and iutA-ibe were associated with group D. CONCLUSIONS: The isolated uropathogens were highly resistant, and the E. coli isolates possessed varying VFs. Continuous monitoring of bacteria associated with UTI in diabetics is highly recommended.202135757820
348260.9565Metagenomic profiling of ARGs in airborne particulate matters during a severe smog event. Information is currently limited regarding the distribution of antibiotic resistance genes (ARGs) in smog and their correlations with airborne bacteria. This study characterized the diversity and abundance of ARGs in the particulate matters (PMs) of severe smog based on publicly available metagenomic data, and revealed the occurrence of 205 airborne ARG subtypes, including 31 dominant ones encoding resistance to 11 antibiotic types. Among the detectable ARGs, tetracycline, β-lactam and aminoglycoside resistance genes had the highest abundance, and smog and soil had similar composition characteristics of ARGs. During the smog event, the total abundance of airborne ARGs ranged from 4.90 to 38.07ppm in PM(2.5) samples, and from 7.61 to 38.49ppm in PM(10) samples, which were 1.6-7.7 times and 2.1-5.1 times of those in the non-smog day, respectively. The airborne ARGs showed complicated co-occurrence patterns, which were heavily influenced by the interaction of bacterial community, and physicochemical and meteorological factors. Lactobacillus and sulfonamide resistance gene sul1 were determined as keystones in the co-occurrence network of microbial taxa and airborne ARGs. The results may help to understand the distribution patterns of ARGs in smog for the potential health risk evaluation.201829751438
133170.9565Serotypes, antibiotic resistance, and virulence genes of Salmonella in children with diarrhea. BACKGROUND: Salmonella is an important foodborne pathogen that causes acute diarrhea in humans worldwide. This study analyzed the relationships of serotypes and antibiotic resistance with virulence genes of Salmonella isolated from children with salmonellosis. METHODS: Serological typing was performed using the slide-agglutination method. The Kirby-Bauer disk diffusion method was used to test antibiotic susceptibility. Twenty virulence genes were detected by PCR. RESULTS: Salmonella Typhimurium (21 isolates, 34.43%) and S Enteritidis (12 isolates, 19.67%) were the predominant species among the 61 isolates. Ampicillin resistance was most common (63.93%), and among the cephalosporins, resistance was most often found to cefotaxime, a third-generation cephalosporin (19.67%). Among the 20 virulence genes, prgH, ssrB, and pagC were detected in all Salmonella isolates. In S Typhimurium, the detection rates of hilA, sipB, marT, mgtC, sopB, pagN, nlpI, bapA, oafA, and tolC were high. In S Enteritidis, the detection rates of icmF, spvB, spvR, and pefA were high. Nitrofurantoin resistance was negatively correlated with the virulence gene bapA (P = .005) and was positively correlated with icmF, spvB, spvR, and pefA (P = .012, .008, .002, and .005, respectively), The P values between all other virulence genes and antibiotic resistance were >.05. CONCLUSION: Salmonella Typhimurium and S Enteritidis were the main serotypes in children with diarrhea in Hangzhou, China. Salmonella exhibited a high level of resistance to common antibiotics, and a high rate of bacteria carrying virulence genes was observed. However, no significant correlation was found between virulence genes and resistance to common antibiotics.202032797660
716480.9564Anthropogenic pressures amplify high-risk antibiotic resistome via co-selection among biocide resistance, virulence, and antibiotic resistance genes in the Ganjiang River basin: Drivers diverge in densely versus sparsely populated reaches. As the largest river in the Poyang Lake system, the Ganjiang River faces escalating anthropogenic pressures that amplify resistance gene dissemination. This study integrated antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and virulence factor genes (VFGs) to reveal their co-selection mechanisms and divergent environmental drivers between densely (DES) and sparsely populated (SPAR) regions of the Ganjiang River basin. The microbial and viral communities and structures differed significantly between the DES and SPAR regions (PERMANOVA, p < 0.001). Midstream DES areas were hotspots for ARGs/BRGs/VFGs enrichment, with peak enrichment multiples reaching 10.2, 5.7, and 5.9-fold respectively. Procrustes analysis revealed limited dependence of ARGs transmission on mobile genetic elements (MGEs) (p > 0.05). Separately, 74 % of dominant ARGs (top 1 %) showed strong correlations with BRGs (r(2) = 0.973, p < 0.01) and VFGs (r(2) = 0.966, p < 0.01) via co-selection. Pathogenic Pseudomonas spp. carrying multidrug-resistant ARGs, BRGs, and adhesion-VFGs were identified as high-risk vectors. In SPAR areas, anthropogenic pressure directly dominated ARGs risk (RC = 54.2 %, β = 0.39, p < 0.05), with biological factors as secondary contributors (RC = 45.8 %, β = 0.33, p < 0.05). In contrast, DES regions showed anthropogenic pressure exerting broader, enduring influences across microorganisms, physicochemical parameters, and biological factors, escalating ARGs risks through diverse pathways, with BRGs/VFGs acting as direct drivers. This study proposes establishing a risk prevention system using BRGs and pathogenic microorganisms as early-warning indicators.202540858019
524490.9560Potentially pathogenic bacteria and antimicrobial resistance in bioaerosols from cage-housed and floor-housed poultry operations. BACKGROUND: Antibiotics are used in animal confinement buildings, such as cage-housed (CH) and floor-housed (FH) poultry operations, to lower the likeliness of disease transmission. In FH facilities, antibiotics may also be used at sub-therapeutic levels for growth promotion. Low levels of antibiotic create a selective pressure toward antimicrobial resistance (AMR) in chicken fecal bacteria. OBJECTIVE: The objective of this study was to compare bacteria and AMR genes in bioaerosols from CH and FH poultry facilities. METHODS: Bioaerosols were collected from 15 CH and 15 FH poultry operations, using stationary area samplers as well as personal sampling devices. Bacteria concentrations were determined by genus- or species-specific quantitative polymerase chain reaction (PCR) and AMR genes were detected using endpoint PCR. RESULTS: Enterococcus spp., Escherichia coli, and Staphylococcus spp. were significantly higher in bioaerosols of FH poultry operations than CH bioaerosols (P < 0.001) while Clostridium perfringens was significantly higher in area bioaerosols of CH operations than FH area bioaerosols (P < 0.05). Campylobacter spp. were detected only in bioaerosols of FH facilities. Zinc bacitracin resistance gene, bcrR, erythromycin resistance gene, ermA, and tetracycline resistance gene, tetA/C, were more prevalent in bioaerosols of FH facilities than CH bioaerosols (P < 0.01, P < 0.01, and P < 0.05, respectively). CONCLUSIONS: Most bacteria are more concentrated and most AMR genes are more prevalent in bioaerosols of FH poultry operations, where growth-promoting antibiotics may be used.201222156572
1288100.9559Assessment of virulence factors and antimicrobial resistance among the Pseudomonas aeruginosa strains isolated from animal meat and carcass samples. BACKGROUND: Pseudomonas aeruginosa bacteria are emerging causes of food spoilage and foodborne diseases. Raw meat of animal species may consider a reservoir of P. aeruginosa strains. OBJECTIVES: The present survey was done to assess the prevalence, antibiotic resistance properties and distribution of virulence factors among the P. aeruginosa strains isolated from raw meat and carcass surface swab samples of animal species. METHODS: Five hundred and fifty raw meat and carcass surface swab samples were collected from cattle and sheep species referred to as slaughterhouses. P. aeruginosa bacteria were identified using culture and biochemical tests. The pattern of antibiotic resistance was determined by disk diffusion. The distribution of virulence and antibiotic resistance genes was determined using polymerase chain reaction. RESULTS: Forty-seven of 550 (8.54%) examined samples were contaminated with P. aeruginosa. The prevalence of P. aeruginosa in raw meat and carcass surface swab samples were 6.57 and 12%, respectively. P. aeruginosa isolates showed the maximum resistance rate toward penicillin (87.23%), ampicillin (85.10%), tetracycline (85.10%), gentamicin (65.95%) and trimethoprim (57.44%). The most commonly detected antibiotic resistance genes were BlaCTX-M (53.19%), blaDHA (42.55%) and blaTEM (27.65%). The most commonly detected virulence factors was ExoS (42.55%), algD (31.91%), lasA (31.91%), plcH (31.91%) and exoU (25.53%). CONCLUSIONS: Meat and carcass surface swab samples may be sources of resistant and virulent P. aeruginosa, which pose a hygienic threat in their consumption. However, further investigations are required to identify additional epidemiological features of P. aeruginosa in meat and carcass surface samples.202336418165
1254110.9559Genetic diversity and antimicrobial resistance of Staphylococcus aureus from recurrent tonsillitis in children. The aim of this study was to analyze the prevalence of Staphylococcus aureus in the tonsils of children subjected tonsillectomy due to recurrent tonsilitis and to determine the spa types of the pathogens, carriage of virulence genes and antimicrobial resistance profiles. The study included 73 tonsillectomized children. Bacteria, including S. aureus were isolated from tonsillar surface prior to tonsillectomy, recovered from tonsillar core at the time of the surgery, and from posterior pharynx 2-4 weeks after the procedure. Staphylococcus aureus isolates were compared by spa typing, tested for antimicrobial susceptibility and for the presence of superantigenic toxin genes (sea-seu, eta, etb, tst, lukS/lukF-PV) by multiplex polymerase chain reaction. Seventy-three patients (mean 7.1 ± 4.1 years, 61.6% male) were assessed. The most commonly isolated bacteria were S. aureus. The largest proportion of staphylococcal isolates originated from tonsillar core (63%), followed by tonsillar surface (45.1%) and posterior pharynx in tonsillectomized children (18.2%, p = 0.007). Five (6.3%) isolates were identified as MRSA (mecA-positive). Up to 67.5% of the isolates synthesized penicillinases (blaZ-positive isolates), and 8.8% displayed MLS(B) resistance. The superantigenic toxin genes were detected in more than half of examined isolates (56.3%). spa types t091, t084, and t002, and clonal complexes (CCs) CC7, CC45, and CC30 turned out to be most common. Staphylococcus aureus associated with RT in children showed pathogenicity potential and considerable genetic diversity, and no clones were found to be specific for this condition although further studies are needed.202031692060
1406120.9559Multicentre study of the burden of multidrug-resistant bacteria in the aetiology of infected diabetic foot ulcers. BACKGROUND: Infected diabetic foot ulcer (IDFU) is a public health issue and the leading cause of non-traumatic limb amputation. Very few published data on IDFU exist in most West African countries. OBJECTIVE: The study investigated the aetiology and antibacterial drug resistance burden of IDFU in tertiary hospitals in Osun state, Nigeria, between July 2016 and April 2017. METHODS: Isolates were cultured from tissue biopsies or aspirates collected from patients with IDFU. Bacterial identification, antibiotic susceptibility testing and phenotypic detection of extended-spectrum beta-lactamase and carbapenemase production were done by established protocols. Specific resistance genes were detected by polymerase chain reaction. RESULTS: There were 218 microorganisms isolated from 93 IDFUs, comprising 129 (59.2%) Gram-negative bacilli (GNB), 59 (27.1%) Gram-positive cocci and 29 (13.3%) anaerobic bacteria. The top five facultative anaerobic bacteria isolated were: Staphylococcus aureus (34; 15.6%), Escherichia coli (23; 10.6%), Pseudomonas aeruginosa (20; 9.2%), Klebsiella pneumoniae (19; 8.7%) and Citrobacter spp. (19; 8.7%). The most common anaerobes were Bacteroides spp. (7; 3.2%) and Peptostreptococcus anaerobius (6; 2.8%). Seventy-four IDFUs (80%) were infected by multidrug-resistant bacteria, predominantly methicillin-resistant S. aureus and GNB producing extended-spectrum β-lactamases, mainly of the CTX-M variety. Only 4 (3.1%) GNB produced carbapenemases encoded predominantly by bla (VIM). Factors associated with presence of multidrug-resistant bacteria were peripheral neuropathy (adjusted odds ratio [AOR] = 4.05, p = 0.04) and duration of foot infection of more than 1 month (AOR = 7.63, p = 0.02). CONCLUSION: Multidrug-resistant facultative anaerobic bacteria are overrepresented as agents of IDFU. A relatively low proportion of the aetiological agents were anaerobic bacteria.202133824857
5247130.9558Similar Levels of Antimicrobial Resistance in U.S. Food Service Ground Beef Products with and without a "Raised without Antibiotics" Claim. U.S. ground beef with "raised without antibiotics" (RWA) label claims are perceived as harboring fewer bacteria with antimicrobial resistance (AMR) than are found in conventional (CONV) ground beef with no such label claim. A total of 370 ground beef samples from CONV ( n = 191) and RWA ( n = 179) production systems were collected over 13 months from three food service suppliers. The following bacteria were cultured: Escherichia coli, tetracycline-resistant (TET(r)) E. coli, third-generation cephalosporin-resistant (3GC(r)) E. coli, Salmonella enterica, TET(r) S. enterica, 3GC(r) S. enterica, nalidixic acid-resistant S. enterica, Enterococcus spp., erythromycin-resistant Enterococcus spp., TET(r) Enterococcus spp., Staphylococcus aureus, and methicillin-resistant S. aureus. TET(r) E. coli was more frequently detected in CONV ground beef (CONV, 54.2%; RWA, 35.2%; P < 0.01), but supplier ( P < 0.01) and production system × suppler interaction ( P < 0.01) effects were also significant. Metagenomic DNA was isolated from each sample, and equal amounts of metagenomic DNA were pooled by supplier, month, and production system for 75 pooled samples (38 CONV, 37 RWA). The abundance of aac(6')-Ie-aph(2″)-Ia, aadA1, bla(CMY-2), bla(CTX-M), bla(KPC-2), erm(B), mecA, tet(A), tet(B), and tet(M) genes was assessed by quantitative PCR. The tet(A) (2.9-log(2)-fold change, P = 0.04) and tet(B) (5.6-log(2)-fold change) ( P = 0.03) genes were significantly more abundant in RWA ground beef. Phylogenetic analyses revealed that ground beef microbiomes differed more by supplier than by production system. These results were consistent with prior research suggesting antimicrobial use in U.S. beef cattle has minimal impact on the AMR of bacteria found in these products. These results should spur a reevaluation of assumptions regarding the impact of antimicrobial use during U.S. beef production on the AMR of bacteria in ground beef.201830476443
5246140.9557Food Service Pork Chops from Three U.S. Regions Harbor Similar Levels of Antimicrobial Resistance Regardless of Antibiotic Use Claims. Pork products from animals "raised without antibiotics" (RWA) are assumed to harbor lower levels of antimicrobial resistance (AMR) than conventional (CONV) pork products with no claims regarding use of antimicrobial agents during production. A total of 372 pork chop samples from CONV (n = 190) and RWA (n = 182) production systems were collected over 13 months from three food service suppliers. The following bacteria were cultured: Escherichia coli, tetracycline-resistant (TET(r)) E. coli, third-generation cephalosporin-resistant (3GC(r)) E. coli, Salmonella enterica, TET(r) Salmonella, 3GC(r) Salmonella, nalidixic acid-resistant Salmonella, Enterococcus spp., TET(r) Enterococcus, erythromycin-resistant Enterococcus, Staphylococcus aureus, and methicillin-resistant S. aureus. Production system did not significantly impact the detection of cultured bacteria (P > 0.05). Metagenomic DNA was isolated from each sample, and equal amounts of metagenomic DNA were pooled by supplier, month, and production system for 75 pooled samples (38 CONV, 37 RWA). Quantitative PCR was used to assess the abundances of the following 10 AMR genes: aac(6')-Ie-aph(2″)-Ia, aadA1, bla(CMY-2), bla(CTX-M), bla(KPC-2), erm(B), mecA, tet(A), tet(B), and tet(M). For all 10 AMR genes, abundances did not differ significantly (P > 0.05) between production systems. These results suggest that use of antimicrobial agents during swine production minimally impacts the AMR of bacteria in pork chops.201931532250
1339150.9557Helicobacter pylori in a poultry slaughterhouse: Prevalence, genotyping and antibiotic resistance pattern. Although Helicobacter pylori (H. pylori) is a highly significant pathogen, its source remains unclear. Many people consume chicken daily as a source of animal protein worldwide; thus, hygienic methods of supplying chickens for consumption are critical for public health. Therefore, our study examined the distribution of the glmM (ureC), babA2, vacA and cagA virulence genes in H. pylori strains in chicken meat and giblets (gizzards and livers) and the resistance of the strains to various antibiotics. Ninety chicken meat, gizzard and liver samples were obtained from a semi-automatic abattoir in Sadat City, Egypt, and were cultured and preliminarily analyzed using biochemical tests. The presence of the ureC, babA2, vacA and cagA genotypes was tested for in samples positive for H. pylori by multiplex polymerase chain reaction (Multiplex-PCR). The resistance of H. pylori to various antimicrobial drugs was tested using the disc diffusion method. In total, 7 of the 90 chicken samples were positive for H. pylori (7.78%); in 3/7 (42.85%) samples, the bacteria were found in the chicken liver, while the bacteria were found in the meat in 2/7 (28.57%) and in the gizzard in 2/7 (28.57%) samples. The total prevalence of both the ureC and babA2 genes in the isolated H. pylori strains was 100%, while the prevalence of the vacA and cagA genes was 57.1% and 42.9%, respectively. The resistance of H. pylori to the antibiotics utilized in our study was 100% for streptomycin; 85.7% for amoxicillin and penicillin; 71.4% for oxytetracycline, nalidixic acid and ampicillin; 57.1% for sulfamethoxazole and erythromycin; and 42.9% for neomycin, chloramphenicol and norfloxacin. In conclusion, the chicken meat and giblets were tainted by H. pylori, with a higher occurrence of the ureC, babA2, vacA and cagA genotypes. Future investigations should investigate the resistance of H. pylori to various antimicrobial agents in Egypt.201830174504
3485160.9556Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach. In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.202133913739
3068170.9555Metagenomic profiling of pigeon faecal microbiota: insights into microbial diversity, pathogens, and antimicrobial resistance genes. Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. This study utilised shotgun metagenomic sequencing to analyse pigeon faecal microbiota and identify potential pathogens. Fresh faecal samples (273) were collected within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. Total genome and viral genomes were extracted and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. The microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, indicating potential enteric-like issues within the pigeon flocks. Approximately 5.11% of the bacterial community (comprising 38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected, primarily associated with pathogenic Shigella, Salmonella, and Klebsiella. The presence of AMR genes and possible co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.202540833454
1340180.9555Prevalence, Virulence, and Antimicrobial Resistance of Campylobacter spp. in Raw Milk, Beef, and Pork Meat in Northern Poland. The purpose of this study was to determine whether raw milk, unpasteurized dairy products, pork, and beef available for sale in the Kujawsko-Pomorskie and Wielkopolska regions in Poland are contaminated with Campylobacter spp. bacteria and may be a potential source of infection. For isolated strains, antibiotic susceptibility and the presence of genes responsible for virulence were examined. Material for research included 1058 food samples collected between 2014 and 2018 with 454 samples of raw milk and unpasteurized dairy products (milk from vending machines, milk from owners of dairy cows, cheese, milk cream) and 604 samples of raw meat (pork, beef). The results indicated that 9.3% of the samples were positive for Campylobacter spp., and Campylobacter jejuni was predominant in this study. Campylobacter bacteria was not found in milk collected from vending machines, as well as cheese and milk cream samples. Campylobacter was noted in 12.7% of beef samples, 11.8% of raw milk purchased from individual suppliers, and 10.9% of pork samples. Resistance to erythromycin (2.0%), azithromycin (3.1%), gentamicin (4.1%), tetracycline (65.3%), and ciprofloxacin (71.4%) was determined using the disc diffusion method. Furthermore, the prevalence of racR, sodB, csrA, virB11, cdtB, iam, and wlaN genes were examined using the PCR method. The sodB, csrA, and cdtB genes exhibited the highest detection rate, but none of the genes were identified in 100% of the isolates. Statistically significant differences between the presence of virulence marker genes, including for iam, racR, and csrA markers, were noted among different sources of the isolates. Differences in the distribution of iam, wlaN, and virB11 were also shown between C. jejuni and C. coli strains. As a result of the analysis, it has been concluded that unpasteurized milk, beef, and pork could be a sources of Campylobacter pathogens. Moreover, this study revealed virulent properties of Campylobacter isolated from such food products and high resistance rates to fluoroquinolones, which may represent difficulties in campylobacteriosis treatment.201931533265
1281190.9555Antibiotic resistance in the pathogenic foodborne bacteria isolated from raw kebab and hamburger: phenotypic and genotypic study. BACKGROUND: In recent years, interest in the consumption of ready-to-eat (RTE) food products has been increased in many countries. However, RTE products particularly those prepared by meat may be potential vehicles of antibiotic-resistance foodborne pathogens. Considering kebab and hamburger are the most popular RTE meat products in Iran, this study aimed to investigate the prevalence and antimicrobial resistance of common foodborne pathogens (Escherichia coli, Salmonella spp., Staphylococcus aureus, and Listeria monocytogenes) in raw kebab and hamburger samples collected from fast-food centers and restaurants. Therefore, total bacterial count (TBC), as well as the prevalence rates and antibiogram patterns of foodborne pathogens in the samples were investigated. Also, the presence of antibiotic-resistance genes (bla(SHV), bla(TEM,) bla(Z), and mecA) was studied in the isolates by PCR. RESULTS: The mean value of TBC in raw kebab and hamburger samples was 6.72 ± 0.68 log CFU/g and 6.64 ± 0.66 log CFU/g, respectively. E. coli had the highest prevalence rate among the investigated pathogenic bacteria in kebab (70%) and hamburger samples (48%). Salmonella spp., L. monocytogenes, and S. aureus were also recovered from 58, 50, and 36% of kebab samples, respectively. The contamination of hamburger samples was detected to S. aureus (22%), L. monocytogenes (22%), and Salmonella spp. (10%). In the antimicrobial susceptibility tests, all isolates exhibited high rates of antibiotic resistance, particularly against amoxicillin, penicillin, and cefalexin (79.66-100%). The bla(TEM) was the most common resistant gene in the isolates of E. coli (52.54%) and Salmonella spp. (44.11%). Fourteen isolates (23.72%) of E. coli and 10 isolates (29.41%) of Salmonella spp. were positive for bla(SHV). Also, 16 isolates (55.17%) of S. aureus and 10 isolates (27.27%) of L. monocytogenes were positive for mecA gene. CONCLUSIONS: The findings of this study showed that raw kebab and hamburger are potential carriers of antibiotic-resistance pathogenic bacteria, which can be a serious threat to public health.202134615465