Aminoglycoside Resistance Research Articles

Genotype MTBDRsl version 2 and phenotypic drug resistance detection of Mycobacterium tuberculosis for fluoroquinolones and aminoglycosides.

Information on genotypic with comparison of phenotypic drug sensitivity test of anti-tuberculosis (TB) has been reported in several studies, which have variable results. The present study aimed to assess the Genotype MTBDRsl version 2.0/Line probe assay (LPA) for the detection of fluoroquinolones (FQ) and aminoglycosides (AMGs) resistance mutations among drug-resistant Mycobacterium TB (MTB) strains and also to compare the patterns of genotypic mutations of gyrA/B, rrs, and eis with mycobacteria growth indicator tube (MGIT 960). A total of 1416 samples were subjected to Genotype MTBDRsl version 2.0 assay. One hundred and twenty sputum smear positive MTB isolates and 37 sputum smear negative MTB isolates confirmed multiple drug resistance resistant to FQ and AMG by the Genotype MTBDRsl version 2.0 were subjected to phenotypic drug susceptibility testing (DST) were analyzed. The association sensitivity, specificity, positive predictive value, negative predictive value, and accuracy for the resistance detection between MGIT (DST) and the Genotype MTBDRsl version 2.0 assay was significant (P < 0.01) of moxifloxacin (MFX) concentration. Sensitivity and specificity value for kanamycin (KAN) resistance was 76% and 89%; 47% and 94% for capreomycin (CAP); and 60% and 76% for low-level KAN, respectively. Our results indicate that MFX (0.25and 1 μg/mL), KAN (2.5 μg/mL), and CAP (2.5 μg/mL) significantly (P < 0.01) and support the World Health Organization guidance to test FQ and AMG by genotypic test.

Metagenomics insights into the effects of lactic acid bacteria inoculation on the biological reduction of antibiotic resistance genes in alfalfa silage

Antibiotic resistance genes (ARGs) are a new type of pollutant and pose major threats to public health. However, the distribution and transmission risk of ARGs in alfalfa silage as the main forage for ruminants have not been studied. This study first deciphered the effects of Lactobacillus plantarum MTD/1 or Lactobacillus buchneri 40788 inoculations on distribution and transmission mechanism of ARGs in alfalfa silage by metagenomics. Results showed that multidrug and bacitracin resistance genes were the dominant ARGs in ensiled alfalfa. The natural ensiling process increased the abundances of bacitracin, beta_lactam, and aminoglycoside in alfalfa silage with 30% DM, and vancomycin in alfalfa silage with 40% DM. Meanwhile, prolonged wilting increased ARG enrichment in fresh alfalfa. Interestingly, alfalfa silage inoculated with L. plantarum MTD/1 or L. buchneri 40788 reduced the abundances of total ARG, and multidrug, MLS, vancomycin, aminoglycoside, tetracycline, and fosmidomycin resistance genes by reductions of the host bacteria and the enrichment of ARGs located in the plasmid. The hosts of ARG in alfalfa silage were mainly derived from harmful bacteria or pathogens, and some of the clinical ARGs were observed in alfalfa silage. Basically, the combined effect of microbes, MGEs, and fermentation quality was the major driver of ARG transfer and dissemination in microecosystem of ensiling, where the microbes appeared to be the crucial factor. In summary, inoculation with the present lactic acid bacteria could reduce ARG abundance in ensiled alfalfa, and a better effect was observed in L. plantarum-treated silage than in L. buchneri treated silage.

Plasmid Composition, Antimicrobial Resistance and Virulence Genes Profiles of Ciprofloxacin- and Third-Generation Cephalosporin-Resistant Foodborne Salmonella enterica Isolates from Russia

Salmonella enterica is an important foodborne pathogen worldwide. Ciprofloxacin and extended-spectrum cephalosporins are the common first-line antimicrobial drugs for the treatment of salmonellosis, antimicrobial resistance genes for which are mostly transferred via plasmids. The goal of this work was to perform genomic analysis of plasmids from foodborne S. enterica isolates obtained in Russia based on whole-genome sequencing. In the current study, 11 multidrug-resistant samples isolated in 2021 from 8 regions of Russia were selected based on their resistance to ciprofloxacin and third-generation cephalosporins (CIP-3rd). Whole-genome short-read sequencing (WGS) was performed for all isolates; the samples belonged to five different sequence types (ST32, ST469, ST11, ST142, and ST548) which had different profiles of antimicrobial resistance (AMR) and virulence genes. We have performed additional long-read sequencing of four representative S. enterica isolates, which showed that they carried pESI-like megaplasmids of 202-280 kb length harboring extended-spectrum β-lactamase genes, fluoroquinolone, tetracycline, and aminoglycosides resistance genes, as well as several virulence determinants. We believe that the WGS data obtained will greatly facilitate further studies of foodborne S. enterica isolates epidemiology in terms of their self-transmissible plasmid composition that mediated antimicrobial resistance and virulence determinants conferring selective advantages of this important bacterial pathogen.

High-pressure processing effect on conjugal antibiotic resistance genes transfer in vitro and in the food matrix among strains from starter cultures

This study analyzed the effect of high-pressure processing (HPP) on the frequency of conjugal gene transfer of antibiotic resistance genes among strains obtained from starter cultures. Gene transfer ability was analyzed in vitro and in situ in the food matrix. It was found that the transfer of aminoglycoside resistance genes did not occur after high-pressure treatment, either in vitro or in situ. After exposure to HPP, the transfer frequencies of tetracycline, ampicillin and chloramphenicol resistance genes increased significantly compared to the control sample, both in vitro and in situ. The frequency of resistance genes transfer in the food matrix in the pressurized samples did not differ significantly from the in vitro transfer rate. Minimum Inhibitory Concentrations (MICs) for these antibiotics determined for transconjugants were lower or equal to MICs determined for the donors. No significant differences were observed between the MIC values determined for the transconjugants obtained in vitro and in situ. The results suggest that HPP may contribute to the spread of antibiotic resistance. This points to the need to verify starter cultures strains for their antibiotic resistance and pressurization parameters to avoid spreading antibiotic resistance genes.

Occurrence, antibiogram, high-level vancomycin and aminoglycosides resistance and potential virulence factors of enterococci in dogs in Nigeria

AbstractThis study was conducted to isolate enterococci from dogs in Nigeria, and to determine the potential virulence, antibiotic susceptibility, phenotypic vancomycin (VAN), high-level ampicillin (AMP) and aminoglycosides susceptibility profile of the isolates. Rectal swabs were collected from 295 randomly-selected, clinically-healthy dogs. The isolation of enterococci was done using Slanetz and Bartley enterococcal selective medium. The resistance of 150 non-repetitive isolates was determined using disc diffusion method. VAN resistance was assessed by high-level disc diffusion and agar-screening methods. High-level AMP and aminoglycosides (gentamicin and streptomycin) resistance was determined by agar-screening method. Potential virulence factors were assayed using phenotypic methods. Out of 295 samples, 234 (80.7%) gave positive growth. From these, 250 enterococcal isolates comprised 229 (91.6%) non-pigmented and 21 (8.4%) pigmented strains, were obtained. Resistance of the isolates was 89% to erythromycin, 92% to rifampicin, 77% to chloramphenicol, 83% to tetracycline, 64% to ciprofloxacin, 32.7% to VAN, 24.7% to high-level streptomycin (HLS) and 6% to high-level gentamicin (HLG). Among 150 non-repetitive resistant isolates, 144 (96%), including all the VAN-, HLS- and HLG-resistant strains, exhibited resistance to at least 3 classes of antibiotics. The mean multiple antibiotic resistance index was 0.54 (range = 0.22 – 0.89). Of these 150 isolates, 94 (62.7%), including all the VAN-, HLS- and HLG-resistant strains, displayed virulence potentials as biofilm (44.7%), surface-layer (13.8%), haemolysin (21.3%), gelatinase (40.4%), caesinase (10.6%) and deoxyribonuclease (12.8%) activities. This study showed that dogs in Nigeria are potential reservoirs and disseminators of potentially-virulent, multidrug-, VAN- and high-level aminoglycosides-resistant enterococci.

The gut microbiome of the healthy population in Kolkata, India, is a reservoir of antimicrobial resistance genes emphasizing the need of enforcing antimicrobial stewardship.

Antimicrobial resistance (AMR) alleviation warrants antimicrobial stewardship (AS) entailing indispensability of epidemiological surveillance. We undertook a small-scale surveillance in Kolkata to detect the presence of antimicrobial resistance genes (ARGs) in the healthy gut microbiome. We found that it was a reservoir of ARGs against common antibiotics. A targeted PCR and sequencing-based ARGs detection against tetracyclines, macrolides, trimethoprim, sulfamethoxazole, aminoglycosides, amphenicol and mobile genetic element (MGE) markers was deployed in twenty-five fecal samples. Relative abundance and frequency of ARGs was calculated. We detected markers against all these classes of antibiotics. 100% samples carried aminoglycoside resistance marker and int1U. A comparison with our previously published diarrheal resistome from the same spatial and temporal frame revealed that a higher diversity of ARGs were detected in the community and a higher rate of isolation of tetC, msrA, tmp and sul-2 was found. The presence of common markers in the two cohorts proves that the gut microbiome has been contaminated with ARGs and which are being disseminated among different ecosystems. This is an issue of discerning concern for public health. The study raises an alarming picture of the AMR crisis in low-middle and emergent economies. It emphasizes the strict enforcement of AS in the community.

Gene-Gene Interactions Reduce Aminoglycoside Susceptibility of Pseudomonas aeruginosa through Efflux Pump-Dependent and -Independent Mechanisms.

Pseudomonas aeruginosa causes a wide range of acute and chronic infections. Aminoglycosides are a cornerstone of treatment, but isolates are often resistant. The purpose of this research was to better understand the genetic basis of aminoglycoside resistance in P. aeruginosa. Bioinformatic approaches identified mutations in resistance-associated genes in the clinical isolates of P. aeruginosa. The common mutations were then engineered into the genome of P. aeruginosa reference strain PAO1. Mutations in the elongation factor gene fusA1 caused the biggest reduction in aminoglycoside susceptibility, with mutations in the two-component regulator gene amgS and the efflux pump regulator gene mexZ having less impact. This susceptibility was further reduced by combinations of mutations. Mutations in fusA1, amgS and mexZ all increased the expression of the mexXY efflux pump that is strongly associated with aminoglycoside resistance. Furthermore, the fusA1 amgS mexZ triple mutant had the highest efflux pump gene expression. Engineering fusA1 and amgS mutants lacking this efflux pump showed that fusA1 and amgS also reduce aminoglycoside susceptibility through additional mechanisms. The fusA1 and amgS mutations reduced bacterial growth, showing that these mutations have a fitness cost. Our findings demonstrate the complex interplay between mutations, efflux pump expression and other mechanisms for reducing the susceptibility of P. aeruginosa to aminoglycosides.

Molecular characterization of antimicrobial resistance related genes in E. coli, Salmonella and Klebsiella isolates from broilers in the West Region of Cameroon.

Antibiotic resistance has become an enduring threat to human health. This has prompted extensive research to identify the determinants responsible in a bid to fight the spread of resistance and also develop new antibiotics. However, routine procedures focus on identifying genetic determinants of resistance only on phenotypically resistant isolates. We aimed to characterise plasmid mediated resistance determinants in key Enterobacteriaceae isolates with differential phenotypic susceptibility profiles and evaluated the contribution of resistance genes on phenotypic expression of susceptibility. The study was carried out on 200 Enterobacteriaceae isolates belonging to the genera E. coli, Salmonella, and Klebsiella; 100 resistant and 100 susceptible to quinolones, aminoglycosides, and ESBL-producing as determined by disk diffusion. Reduced susceptibility in susceptible isolates was determined as an increased MIC by broth microdilution. Plasmid-borne resistance genes were sought in all isolates by endpoint PCR. We performed correlations tests to determine the relationship between the occurrence of resistance genes and increased MIC in susceptible isolates. We then used the notion of penetrance to show adequacy between resistance gene carriage and phenotypic resistance as well as diagnostic odds ratio to evaluate how predictable phenotypic susceptibility profile could determine the presence of resistant genes in the isolates. Reduced susceptibility was detected in 30% (9/30) ESBL negative, 50% (20/40) quinolone-susceptible and 53.33% (16/30) aminoglycoside-susceptible isolates. Plasmid-borne resistance genes were detected in 50% (15/30) of ESBL negative, 65% (26/40) quinolone susceptible and 66.67% (20/30) aminoglycoside susceptible isolates. Reduced susceptibility increased the risk of susceptible isolates carrying resistance genes (ORs 4.125, 8.36, and 8.89 respectively for ESBL, quinolone, and aminoglycoside resistance genes). Resistance gene carriage correlated significantly to reduced susceptibility for quinolone and aminoglycoside resistance genes (0.002 and 0.015 at CI95). Gene carriage correlated with phenotypic resistance at an estimated 64.28% for ESBL, 56.90% for quinolone, and 58.33% for aminoglycoside resistance genes. A high carriage of plasmid-mediated genes for ESBL, quinolone, and aminoglycoside resistance was found among the Enterobacteriaceae tested. However, gene carriage was not always correlated with phenotypic expression. This allows us to suggest that assessing genetic determinants of resistance should not be based on AST profile only. Further studies, including assessing the role of chromosomal determinants will shed light on other factors that undermine antimicrobial susceptibility locally.

Functional characterization of a novel aminoglycoside phosphotransferase, APH(9)-Ic, and its variant from Stenotrophomonas maltophilia.

The intrinsic resistance mechanism plays an essential role in the bacterial resistance to a variety of the antimicrobials. The aim of this study is to find the chromosome-encoded novel antimicrobial resistance gene in the clinical isolate. The function of the predicted resistance gene was verified by gene cloning and antibiotic susceptibility test. Recombinant protein expression and enzyme kinetic studies were performed to explore the in vivo activity of the enzyme. Expression of the resistance gene exposed to antimicrobial was determined by RT-qPCR. Whole genome sequencing and bioinformatic analysis were applied to analyze the genetic context of the resistance gene. The novel aminoglycoside (AG) resistance genes designated aph(9)-Ic and aph(9)-Ic1 confer resistance to spectinomycin, and a recombinant strain harboring aph(9)-Ic (pMD19-T-aph(9)-Ic/DH5α) showed a significantly increased minimum inhibitory concentration (MIC) level against spectinomycin compared with the control strains (DH5α and pMD19-T/DH5α). The result of the kinetic analysis of APH(9)-Ic was consistent with the MIC result for the recombinant pMD19-T-aph(9)-Ic/DH5α, showing the efficient catalytic activity for spectinomycin [kcat/Km ratio = (5.58 ± 0.31) × 104 M-1·s-1]. Whole-genome sequencing demonstrated that the aph(9)-Ic gene was located on the chromosome with a relatively conserved genetic environment, and no mobile genetic element was found in its surrounding region. Among all the function-characterized resistance genes, APH(9)-Ic shares the highest amino acid sequence identity of 33.75% with APH(9)-Ia. We characterized a novel AG resistance gene aph(9)-Ic and its variant aph(9)-Ic1 that mediated spectinomycin resistance from S. maltophilia. The identification of the novel AG resistance genes will assist us in elucidating the complexity of resistance mechanisms in microbial populations.

Trends of Antibiotic Resistance in Multidrug-Resistant Pathogens Isolated from Blood Cultures in a Four-Year Period.

Multidrug-resistant organisms cause serious infections with significant morbidity and mortality in the worldwide. These organisms have been identified as urgent and serious threats by CDC. The aim of this study was to determine the prevalence and changes of antibiotic resistance of multidrug-resistant pathogens isolated from blood cultures over a four-year period in a tertiary-care hospital. Blood cultures were incubated in a blood culture system. Positive signalling blood cultures were subcultured on 5% sheep-blood agar. Identification of isolated bacteria was performed using conventional or automated identification systems. Antibiotic susceptibility tests were performed by disc diffusion and/or gradient test methods, if necessary, by automated systems. The CLSI guidelines were used for interpretation of antibiotic susceptibility testing of bacteria. The most frequently isolated Gram-negative bacteria was Escherichia coli (33.4%) followed by Klebsiella pneumoniae (21.5%). ESBL positivity was 47% for E. coli, 66% for K. pneumoniae. Among E. coli, K. pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii isolates, carbapenem resistance was 4%, 41%, 37%, and 62%, respectively. Carbapenem resistance of K. pneumoniae isolates has increased from 25% to 57% over the years, and the highest rate (57%) occured during the pandemic period. It is noteworthy that the aminoglycoside resistance in E. coli isolates gradually increased from 2017 to 2021. The rate of methicillin-resistant S. aureus (MRSA) was found to be 35.5%. Increased carbapenem resistance in K. pneumoniae and A. baumannii isolates is noteworthy, but carbapenem resistance in P. aeruginosa decreased. It is of great importance for each hospital to monitor the increase in resistance in clinically important bacteria, especially isolated from invasive samples, in order to take the necessary precautions in a timely manner. Future studies involving clinical data of patients and bacterial resistance genes are warranted.

Investigation of Salmonella types and its antibiotic resistance profile and determination of parasite carrier in free-living hedgehogs in Istanbul, Türkiye

Hedgehogs, which are kept as pets worldwide, are prohibited from being sold or kept as pets in Türkiye. The aim of the study was to investigate Salmonella and endo-parasite carriage in hedgehogs and to determine the antibacterial resistance profiles of isolated Salmonella agents. Free-range hedgehogs living in parks and gardens of Istanbul that were brought to veterinary clinics by animal lovers for check-up and treatment were used for sampling. Thirty faecal samples were taken from the animals. For bacteriological examinations, samples were seeded on selective media, and then the isolates were identified by conventional methods as Salmonella spp. Identification and antibiotic susceptibilities of the isolates were determined by the BD Phoenix Automated Microbiology System. All faecal samples were also investigated by PCR for Salmonella spp. specific gene regions. The aminoglycoside and quinolone resistance profiles of the strains were analysed by PCR. On parasitological examination, samples were analysed for parasites’ eggs, oocysts, and larvae. Two Salmonella isolates were determined as Salmonella enterica serovar Typhimurium (S. Typhimurium), whose antigenic formula was 4,5,12:i:1,2. The isolates were phenotypically resistant to ciprofloxacin but did not harbour any of the genes examined. Out of 30 faecal samples, 19 (63.3%) were positive for one or more genera of parasites. The hedgehogs were infected with the species of Capillaria spp. (60%), Crenosoma spp. (13.3%), Eimeria spp. (10%) and Acanthocephala spp. (6.6%). This study is the first report of Salmonella carrier and internal parasite fauna of hedgehogs in Istanbul, Türkiye.

Molecular study of Shigella dysenteriae Aminoglycoside Resistance Genes Isolated from Children and its Expression Under the Influence of Curcumin Nanoparticle

Molecular study of <i>Shigella dysenteriae</i> Aminoglycoside Resistance Genes Isolated from Children and its Expression Under the Influence of Curcumin Nanoparticle

OCCURRENCE OF AMINOGLYCOSIDES RESISTANCE GENES ACC(6)-IB AND ACC(3)-II AMONG GRAM-NEGATIVE ISOLATES CAUSING URINARY TRACT INFECTION IN PEDIATRIC PATIENTS, NAJAF, IRAQ.

The aim: The aim of the study was to detect the antimicrobial susceptibility patterns and frequency of aminoglycosides resistance genes of Gram-negative bacteria isolated from pediatric patient with UTI. Materials and methods: The study has been performed with a total of 500 urine specimens collected from pediatric patients under the age of 18 year suspected with UTI, admitted to hospitals in Al-Najaf province/Iraq during the period from November 2018 to March 2019. Results: A total of 500 urine specimens had been tested, 120 (24%) had signifficant bacteriuria, while there 380 (76%) had non-signi!cant bacteriuria. Escherichia coli represent about 70 (68.2%) followed by followed by 23 (22.5%) K. pneumoniae, 5 (4.9%) P. aeruginosa, 2 (1.9%) Proteus spp., 1 (0.9%) Enterobacter spp. and 1 (0.9%) Oligella uratolytic. The antimicrobial susceptibility profile of 102 Gram-negative isolates, revealed that 59 (58%) were multidrug resistant (MDR) and 38(37%) were extensive drug resistant (XDR). The PCR results of aminoglycosides resistance showing that 23 (74.1%) Gram-negative isolates had acc(6')-Ib gene and 12 (38.7%) Gram-negative isolates acc(3')-II gene. Conclusions: A high frequency of multi-drug resistance and extensive-drug resistance of isolates were recognized, and an alarming percentage of amino-glycosides resistance to acc(6')-Ib and acc(3')-II.

Discovery and development of inhibitors of acetyltransferase Eis to combat Mycobacterium tuberculosis.

Aminoglycosides are bactericidal antibiotics with a broad spectrum of activity, used to treat infections caused mostly by Gram-negative pathogens and as a second-line therapy against tuberculosis. A common resistance mechanism to aminoglycosides is bacterial aminoglycoside acetyltransferase enzymes (AACs), which render aminoglycosides inactive by acetylating their amino groups. In Mycobacterium tuberculosis, an AAC called Eis (enhanced intracellular survival) acetylates kanamycin and amikacin. When upregulated as a result of mutations, Eis causes clinically important aminoglycoside resistance; therefore, Eis inhibitors are attractive as potential aminoglycoside adjuvants for treatment of aminoglycoside-resistant tuberculosis. For over a decade, we have studied Eis and discovered several series of Eis inhibitors. Here, we provide a detailed protocol for a colorimetric assay used for high-throughput discovery of Eis inhibitors, their characterization, and testing their selectivity. We describe protocols for in vitro cell culture assays for testing aminoglycoside adjuvant properties of the inhibitors. A procedure for obtaining crystals of Eis-inhibitor complexes and determining their structures is also presented. Finally, we discuss applicability of these methods to discovery and testing of inhibitors of other AACs.

ASSESSMENT OF THE RELATIVE ABUNDANCE OF ANTIBIOTIC RESISTANCE GENES OF BACTERIA IN THE GUT OF PIGLETS (SUS SCROFA DOMESTICUS) IN THE EARLY NEONATAL PERIOD

The article presents the assessment of the presence and relative amount of antibiotic resistance genes of bacteria in the gut microbiome of piglets in the early neonatal period. The genes for beta-lactam antibiotics (penicillins, cephalosporins, carbapenems, monobactams) have become the dominant majority of the antibiotic resistance genes present in both healthy and sick piglets. Tetracycline resistance genes were also found in the samples of healthy and sick animals. Healthy animals had the aminoglycoside resistance gene Aph3-III (relative content - 81.15%). The quinolone antibiotic resistance genes QnrB5 and QnrB19 were present in both healthy and sick animals, and the gene QnrD was identified only in the piglets with diarrhea (relative content - 10.27%). The same relative abundance of the sulfonamide resistance gene SulII (relative content - 82%) was demonstrated in both healthy and sick piglets, while the gene SulIII was found only in the animals with diarrhea (relative content - 13.44%). The results show a wide spread of antibiotic resistance genes in the population of healthy piglets and piglets with diarrhea, and this requires special attention from pig breeding farms in order to minimize further migration of antibiotic resistance genes.

First report on the molecular characteristics of mcr-1 colistin resistant E. coli isolated from retail broiler meat in Bangladesh

Poultry meat is considered as a potential source of colistin resistant Escherichia coli (CREC). This study aimed to determine the prevalence and characteristics of CREC in broiler meat and ascertain their possible zoonotic potential(s). Broiler meat (n = 104) comprising 26 of each of the thigh, breast, liver, and proventriculus-gizzard was purchased from the retail outlets, Bangladesh. CREC was isolated from the meat samples on MacConkey agar plates containing colistin sulfate followed by PCR confirmation, mcr subtyping (mcr-1 to mcr-5), phylogenetic grouping and detailed molecular characterization through whole genome sequencing (WGS). Antimicrobial resistance of the CREC isolates were evaluated by disc diffusion method and MIC (minimum inhibitory concentration) of colistin sulfate was determined by broth microdilution. The investigation revealed 58 (55.77 %) of 104 samples as positive for CREC, and 53 (91.38 %) of CREC isolates carried mcr-1 gene with no other mcr subtypes evident. Most of the CREC belonged to commensal E. coli (66.04 %) with some pathogenic phylotypes (33.96 %) based on dichotomous decision tree. All the mcr-1 CREC isolates were multidrug-resistant (MDR) and had MICs of 4–8 μg/mL colistin sulfate. WGS of a commensal MDR mcr-1 CREC strain 1ChBEc2mcr revealed as a potential human pathogen belonging to ST162 that harbored 60 virulence factors associated genes (VFGs). The mcr-1 gene in 1ChBEc2mcr genome was located on a plasmid (p1ChBEc2mcr) and showed nucleotide similarities (>95 %) to another plasmid reported from human E. coli in Bangladesh. Beyond mcr-1 gene, this plasmid (p1ChBEc2mcr) also harbored genes related to aminoglycoside, beta-lactams, macrolides, and tetracycline resistance. Presence of similar mcr-1 carrying plasmids in broiler and human CREC denotes a threat of possibly human to avian (broiler) or vice-versa transfer of mcr-1 CREC through close contact as prevailing in the retail outlets of Bangladesh.

Diversity of bacteria carrying antibiotic resistance genes in hospital raw sewage in Southeastern Brazil.

In recent decades, antibiotic-resistant bacteria (ARB) emerged and spread among humans and animals worldwide. In this study, we evaluated the presence of ARB and antibiotic resistance genes (ARGs) in the raw sewage of two hospitals in Brazil. Sewage aliquots were inoculated in a selective medium with antibiotics. Bacterial identification was performed by MALDI-TOF and ARGs were assessed by polymerase chain reaction (PCR). A total of 208 strains from both hospitals were isolated (H1 = 117; H2 = 91). A wide variety of Enterobacterales and non-Enterobacterales species were isolated and most of them were Enterobacter spp. (13.0%), Proteus mirabilis (10.1%), and Klebsiella pneumoniae (9.6%). blaTEM and blaKPC were the most frequent β-lactamase-encoding genes and the predominant macrolide resistance genes were mph(A) and mel. Many species had the three tetracycline resistance genes (tetD, tetM, tetA) and strB was the prevalent aminoglycoside resistance gene. Two Staphylococcus haemolyticus strains had the mecA gene. Quinolone, colistin, and vancomycin resistance genes were not found. This study showed that hospital raw sewage is a great ARB and ARG disseminator. Strict monitoring of hospital sewage treatment is needed to avoid the spread of these genes among bacteria in the environment.

Characterization of integrative and conjugative elements carrying antibiotic resistance genes of Streptococcus suis isolated in China.

Streptococcus suis, an emerging zoonotic pathogen, is important reservoirs of antibiotic resistance genes that play critical roles in the horizontal transfer of corresponding resistances. In the present study, 656 antibiotic resistance (AR) genes were detected in 154 of 155 genomes of S. suis strains isolated from the nasopharynx of slaughtered pigs and the lungs of diseased pigs in China. The AR genes were clustered into 11 categories, consisting of tetracycline, macrolides, lincosamide, streptogramin, aminoglycoside, trimethoprim, amphenicols, nucleoside, quinupristin/dalfopristin, glycopeptide, and oxazolidinones resistance genes. In order to investigate the transmission patterns of the AR genes, AR genes-associated the mobile genetic elements (MGEs) were extracted and investigated. Twenty ICEs, one defective ICE, one tandem ICE, and ten prophages were found, which mainly carried tetracycline, macrolides/lincosamides/streptogramin (MLS), and aminoglycosides resistance genes. Three types of DNA cargo with AR genes were integrated into specific sites of ICEs: integrative mobilizable elements (IMEs), cis-IMEs (CIMEs), and transposon Tn916. Obvious differences in AR gene categories were found among the three cargo types. IMEs mainly harbored tetracycline and MLS resistance genes. CIMEs mainly carried aminoglycoside resistance genes, while transposon Tn916 carried only the tet (M) gene. Nearly all AR genes in ICEs were carried by IMEs and CIMEs. IMEs were prevalent and were also detected in additional 29 S. suis genomes. The horizontal transfer of IMEs and CIMEs may play critical role in ICE evolution and AR gene transmission in the S. suis population. Our findings provide novel insights into the transmission patterns of AR genes and the evolutionary mechanisms of ICEs in S. suis.

Study on the drug resistance and pathogenicity of Escherichia coli isolated from calf diarrhea and the distribution of virulence genes and antimicrobial resistance genes.

The unscientific and irrational use of antimicrobial drugs in dairy farms has led to the emergence of more serious drug resistance in Escherichia coli. In this study, cases of calf diarrhea in cattle farms around the Hohhot area were studied, and Escherichia coli were identified by PCR and biochemical methods, while the distribution of virulence and drug resistance genes of the isolates was analyzed. The results showed that 21 strains of Escherichia coli were isolated from the diseased materials, and the isolation rate was 60%. The isolated strains belong to 15 ST types. The drug resistance levels of the isolated strains to 20 kinds of antimicrobial agent viz., penicillin, ampicillin, cefotaxime, cefepime, cefoxitin, and ceftriaxone were more than 50%. The resistance rate to meropenem was 10%. The resistance rates to tetracycline and doxycycline were 33% and 29%, to ciprofloxacin, levofloxacin and enrofloxacin were 48%, 33%, and 33%, to amikacin, kanamycin and gentamicin were 19%, 24% and 38%, to cotrimoxazole and erythromycin were 48% and 15%, to florfenicol, chloramphenicol and polymyxin B were 29%, 33%, and 5%. Nine strains of pathogenic calf diarrhea Escherichia coli were isolated by mouse pathogenicity test. The detection rates of virulence genes for the adhesion class were fimC (95%), IuxS (95%), eaeA (76%), fimA (62%), ompA (52%), and flu (24%). The detection rates for iron transporter protein like virulence genes were iroN (33%), iutA (19%), fyuA (14%), irp5 (9.5%), Iss (9.5%), and iucD (9.5%). The detection rates for toxin-like virulence genes were phoA (90%), Ecs3703 (57%), ropS (33%), hlyF (14%), and F17 (9.5%). The detection rates of tetracycline resistance genes in isolated strains were tetB (29%), tetA (19%) and tetD (14%). The detection rates for fluoroquinolone resistance genes were parC (Y305H, P333S, R355G) (9.5%), gyrA (S83L, D87N) (28%), qnrD (43%), and qnrS (9.5%). The detection rates for β-lactam resistance genes were bla CTX-M (29%), bla TEM (29%), and bla SHV (9.5%). The detection rates for aminoglycoside resistance genes were strA-B (57%), aacC (33%), aac(3')-IIa (29%), and aadAI (24%). The detection rates of chloramphenicol resistance genes floR and sulfa resistance genes sul2 were 24 and 33%. Pathogenic Escherichia coli causing diarrhea in calves contain abundant virulence genes and antibiotic resistance genes.

The antibiotic resistome in Escherichia coli isolated from human, food and animal sources.

The aim of this study was to analyze and compare the prevalence and distribution of resistance genes in Escherichia coli genomes isolated from human clinical samples and animal-based foods worldwide. We download from NCBI Pathogen Detection Database the corresponding metadata of the 7123 E. coli genome to access the information about the antimicrobial resistance gene content. The geographic location and the source of isolation were also obtained and compiled with the antimicrobial resistance gene for statistical analysis, results and discussion. Our criteria considered four groups for analyzing the antimicrobial resistance gene distribution. The first group of genomes from invasive clinical human (ICH) samples from countries with Human Development Index (HDI) ≥ 0.850; the second group of ICH from countries with an HDI≤0.849; the third group of animal-based foods (ABF) from countries with HDI≥0.850 and the fourth group of ABFs from countries with HDI≤0.849. The most prevalent genes in the first group were blaCTX-M-134 (96.53%) and blaCTX-M-27 (86.35%). In the second group, ere(A) (95.96%), soxS (94.49%), qepA8 (90.81%), blaCTX-M-15 (85.66%), and fosA3 (80.88%). In the third group, the most frequently detected were aadA12 (98.5%), ant(3") (89.92%), and blaCARB-2 (87.2%). In the fourth group, aadA12 and aac(3)-IV were identified in 100% of the analyzed genomes. It was clear that the use of aminoglycosides in animal production is increasing the selective pressure on micro-organisms in both groups of countries since genes linked to aminoglycoside resistance are related to E. coli from ABF samples. The genomic profile of E. coli from HDI≥0.850 countries indicates a selective pressure aimed at cephalosporins given the high prevalence in both sources.