Co-resistance: an opportunity for the bacteria and resistance genes

Mobile Colistin-Resistant Genes mcr-1, mcr-2, and mcr-3 Identified in Diarrheal Pathogens among Infants, Children, and Adults in Bangladesh: Implications for the Future

Colistin is a last-resort antimicrobial for treating multidrug-resistant Gram-negative bacteria. Phenotypic colistin resistance is highly associated with plasmid-mediated mobile colistin resistance (mcr) genes. mcr-bearing Enterobacteriaceae have been detected in many countries, with the emergence of colistin-resistant pathogens a global concern. This study assessed the distribution of mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5 genes with phenotypic colistin resistance in isolates from diarrheal infants and children in Bangladesh. Bacteria were identified using the API-20E biochemical panel and 16s rDNA gene sequencing. Polymerase chain reactions detected mcr gene variants in the isolates. Their susceptibilities to colistin were determined by agar dilution and E-test by minimal inhibitory concentration (MIC) measurements. Over 31.6% (71/225) of isolates showed colistin resistance according to agar dilution assessment (MIC > 2 μg/mL). Overall, 15.5% of isolates carried mcr genes (7, mcr-1; 17, mcr-2; 13, and mcr-3, with co-occurrence occurring in two isolates). Clinical breakout MIC values (≥4 μg/mL) were associated with 91.3% of mcr-positive isolates. The mcr-positive pathogens included twenty Escherichia spp., five Shigella flexneri, five Citrobacter spp., two Klebsiella pneumoniae, and three Pseudomonas parafulva. The mcr-genes appeared to be significantly associated with phenotypic colistin resistance phenomena (p = 0.000), with 100% colistin-resistant isolates showing MDR phenomena. The age and sex of patients showed no significant association with detected mcr variants. Overall, mcr-associated colistin-resistant bacteria have emerged in Bangladesh, which warrants further research to determine their spread and instigate activities to reduce resistance.

Widespread prevalence of plasmid-mediated blaCTX-M type extended-spectrum beta-lactamase Escherichia coli in backyard broiler production systems in the United States

Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E. coli. Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E. coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E. coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E. coli. Assessment of ESBL phenotype was determined through using disk diffusion with 3rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E. coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a blaCTX-M gene, the dominant variant being blaCTX-M-1, and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of blaCTX-M type ESBL E. coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition

BACKGROUND

In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age.

RESULTS

We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs.

CONCLUSIONS

We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract.

In Vitro Microevolution and Co-Selection Assessment of Amoxicillin and Cefotaxime Impact on Escherichia coli Resistance Development

The global spread of antimicrobial resistance has become a prominent issue in both veterinary and public health in the 21st century. The extensive use of amoxicillin, a beta-lactam antibiotic, and consequent resistance development are particularly alarming in food-producing animals, with a focus on the swine and poultry sectors. Another beta-lactam, cefotaxime, is widely utilized in human medicine, where the escalating resistance to third- and fourth-generation cephalosporins is a major concern. The aim of this study was to simulate the development of phenotypic and genotypic resistance to beta-lactam antibiotics, focusing on amoxicillin and cefotaxime. The investigation of the minimal inhibitory concentrations (MIC) of antibiotics was performed at 1×, 10×, 100×, and 1000× concentrations using the modified microbial evolution and growth arena (MEGA-plate) method. Our results indicate that amoxicillin significantly increased the MIC values of several tested antibiotics, except for oxytetracycline and florfenicol. In the case of cefotaxime, this increase was observed in all classes. A total of 44 antimicrobial resistance genes were identified in all samples. Chromosomal point mutations, particularly concerning cefotaxime, revealed numerous complex mutations, deletions, insertions, and single nucleotide polymorphisms (SNPs) that were not experienced in the case of amoxicillin. The findings suggest that, regarding amoxicillin, the point mutation of the acrB gene could explain the observed MIC value increases due to the heightened activity of the acrAB-tolC efflux pump system. However, under the influence of cefotaxime, more intricate processes occurred, including complex amino acid substitutions in the ampC gene promoter region, increased enzyme production induced by amino acid substitutions and SNPs, as well as mutations in the acrR and robA repressor genes that heightened the activity of the acrAB-tolC efflux pump system. These changes may contribute to the significant MIC increases observed for all tested antibiotics. The results underscore the importance of understanding cross-resistance development between individual drugs when choosing clinical alternative drugs. The point mutations in the mdtB and emrR genes may also contribute to the increased activity of the mdtABC-tolC and emrAB-tolC pump systems against all tested antibiotics. The exceptionally high mutation rate induced by cephalosporins justifies further investigations to clarify the exact mechanism behind.

Escherichia coli and their potential transmission of carbapenem and colistin-resistant genes in camels

BACKGROUND

Camels harbouring multidrug-resistant Gram-negative bacteria are capable of transmitting various microorganisms to humans. This study aimed to determine the distribution of anti-microbial resistance among Escherichia coli (E. coli) isolated from the feces of apparently healthy camels in Egyptian abattoirs. Additionally, we sought to characterize Shiga toxin-producing E. coli (STEC) strains, assess their virulence potential, and investigate the possibility of camels spreading carbapenem- and colistin-resistant E. coli.

METHODS

121 fecal swaps were collected from camels in different abattoirs in Egypt. Isolation and identification of E. coli were performed using conventional culture techniques and biochemical identification. All isolates obtained from the examined samples underwent genotyping through polymerase chain reaction (PCR) of the Shiga toxin-encoding genes (Stx1 and Stx2), the carbapenemase-encoding genes (blaKPC, blaOXA-48, blaNDM, and blaVIM), and the mcr genes for mcr-1 to mcr-5.

RESULT

Bacteriological examination revealed 75 E. coli isolates. PCR results revealed that one strain (1.3%) tested positive for Stx1, and five (6.6%) were positive for Stx2. Among the total 75 strains of E. coli, the overall prevalence of carbapenemase-producing E. coli was 27, with 7 carrying blaOXA48, 14 carrying blaNDM, and 6 carrying blaVIM. Notably, no strains were positive for blaKPC but a high prevalence rate of mcr genes were detected. mcr-1, mcr-2, mcr-3, and mcr-4 genes were detected among 3, 2, 21, and 3 strains, respectively.

CONCLUSION

The results indicate that camels in Egypt may be a primary source of anti-microbial resistance (AMR) E. coli, which could potentially be transmitted directly to humans or through the food chain.

Effect of ginger essential oil and 6-gingerol on a multispecies biofilm of Listeria monocytogenes, Salmonella Typhimurium, and Pseudomonas aeruginosa

The objective of this study was to evaluate the potential antimicrobial and antibiofilm effect of ginger essential oil (GEO) and 6-gingerol on a multispecies biofilm formed by Listeria monocytogenes, Salmonella Typhimurium, and Pseudomonas aeruginosa on a polypropylene surface. The minimum inhibitory concentration concentrations obtained for GEO were 100 and 50 mg/mL and for 6-gingerol 1.25 mg/mL. Sessile cell counts ranged within 5.35-7.35 log CFU/cm2 in the control biofilm, with the highest sessile growth at 72 h. GEO treatments acted on the total population regardless of concentration at 1 and 48 h. L. monocytogenes behaved similarly to the total population, showing GEO action at 1 h and keeping the same pattern at 48, 72, and 96 h. Better action on S. Typhimurium was obtained at times of 1, 72, and 96 h. P. aeruginosa showed logarithmic reduction only when treated with GEO 50 mg at 24 h. As for 6-gingerol, in general, there was no significant action (p > 0.05) on the evaluated sessile cells. GEO showed antimicrobial activity against L. monocytogenes, S. Typhimurium, and P. aeruginosa, acting as an inhibitor of biofilm formation. As for 6-gingerol, it was considered a possible antimicrobial agent but without efficacy during biofilm formation.

Molecular epidemiology and pathogenomics of extended-spectrum beta-lactamase producing- Escherichia coli and - Klebsiella pneumoniae isolates from bulk tank milk in Tennessee, USA

Introduction

The rise in extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in dairy cattle farms poses a risk to human health as they can spread to humans through the food chain, including raw milk. This study was designed to determine the status, antimicrobial resistance, and pathogenic potential of ESBL-producing -E. coli and -Klebsiella spp. isolates from bulk tank milk (BTM).

Methods

Thirty-three BTM samples were collected from 17 dairy farms and screened for ESBL-E. coli and -Klebsiella spp. on CHROMagar ESBL plates. All isolates were confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and subjected to antimicrobial susceptibility testing and whole genome sequencing (WGS).

Results

Ten presumptive ESBL-producing bacteria, eight E. coli, and two K. pneumoniae were isolated. The prevalence of ESBL-E. coli and -K. pneumoniae in BTM was 21.2% and 6.1%, respectively. ESBL-E. coli were detected in 41.2% of the study farms. Seven of the ESBL-E. coli isolates were multidrug resistant (MDR). The two ESBL-producing K. pneumoniae isolates were resistant to ceftriaxone. Seven ESBL-E. coli strains carry the blaCTX-M gene, and five of them co-harbored blaTEM-1. ESBL-E. coli co-harbored blaCTX-M with other resistance genes, including qnrB19, tet(A), aadA1, aph(3'')-Ib, aph(6)-Id), floR, sul2, and chromosomal mutations (gyrA, gyrB, parC, parE, and pmrB). Most E. coli resistance genes were associated with mobile genetic elements, mainly plasmids. Six sequence types (STs) of E. coli were detected. All ESBL-E. coli were predicted to be pathogenic to humans. Four STs (three ST10 and ST69) were high-risk clones of E. coli. Up to 40 virulence markers were detected in all E. coli isolates. One of the K. pneumoniae was ST867; the other was novel strain. K. pneumoniae isolates carried three types of beta-lactamase genes (blaCTX-M, blaTEM-1 and blaSHV). The novel K. pneumoniae ST also carried a novel IncFII(K) plasmid ST.

Conclusion

Detection of high-risk clones of MDR ESBL-E. coli and ESBL-K. pneumoniae in BTM indicates that raw milk could be a reservoir of potentially zoonotic ESBL-E. coli and -K. pneumoniae.

Implications of different waterfowl farming on cephalosporin resistance: Investigating the role of blaCTX-M-55

We investigated the cephalosporin resistance of Escherichia coli from waterfowl among different breeding mode farms. In 2021, we isolated 200 strains of E. coli from waterfowl feces samples collected from Sichuan, Heilongjiang, and Anhui provinces. The key findings are: Out of the 200 strains, 80, 80, and 40 strains were isolated from waterfowl feces samples in intensive, courtyard, and outdoor breeding mode farms, respectively. The overall positive rate of the ESBL phenotype, detecting by the double disk diffusion method, was 68.00% (136/200). In particular, the rates for intensive, courtyard, and outdoor breeding modes were 98.75%, 36.25%, and 70.00%, respectively. Results of MIC test showed drug resistance rates in the intensive breeding mode: 100.00% for cephalothin, 38.75% for cefoxitin, 100.00% for cefotaxime, and 100.00% for cefepime. In courtyard breeding mode, the corresponding rates were 100.00%, 40.00%, 63.75%, and 45.00%, respectively. In outdoor breeding mode, the corresponding rates were 100.00%, 52.50%, 82.50%, and 77.50%, respectively. The PCR results for blaCTX-M, blaTEM, blaOXA, and blaSHV showed the detection rate of blaCTX-M was highest at 75.50%, with blaCTX-M-55 is the main subtype gene, followed by blaTEM at 73.50%. We screened 58 donor strains carrying blaCTX-M-55, including 52 strains from the intensive breeding mode. These donor bacteria can transfer different plasmids to recipient E. coli J53, resulting in recipient bacteria acquiring cephalosporin resistance, and the conjugational transfer frequency ranged from 1.01 × 10-5 to 6.56 × 10-2. The transferred plasmids remained stable in recipient bacteria for up to several days without significant adaptation costs observed. During molecular typing of E. coli with conjugational transfer ability, the blaCTX-M-55 was found to be widely present in different ST strains with several phylogenetic groups. In summary, cephalosporin resistance of E. coli carried by waterfowl birds in intensive breeding mode farm was significantly higher than in courtyard and outdoor mode farms. The blaCTX-M-55 subtype gene was the prevalent ARGs and can be horizontally transferred through plasmids, which plays a key role in the spread of cephalosporin drug resistance.

Role of Plasmids in Co-Selection of Antimicrobial Resistances Among Escherichia coli Isolated from Pigs

Co-selection is thought to occur when resistance genes are located on the same mobile genetic element. However, this mechanism is currently poorly understood. In this study, complete circular plasmids from swine-derived Escherichia coli were sequenced with short and long reads to confirm that resistance genes involved in co-resistance were co-transferred by the same plasmid. Conjugative transfer tests were performed, and multiple resistance genes were transmitted. The genes possessed by the donor, transconjugant, and plasmid of the donor were highly similar. In addition, the sequences of the plasmid of the donor and the plasmid of the transconjugant were almost identical. Resistance genes associated with statistically significant combinations of antimicrobial use and resistance were co-transmitted by the same plasmid. These results suggest that resistance genes may be involved in co-selection by their transfer between bacteria on the same plasmid.

Anti-MRSA and Biological Activities of Propolis Concentrations Loaded to Chitosan Nanoemulsion for Pharmaceutics Applications

Propolis is a naturally occurring substance with beneficial properties; bees produce it from various plant sources, and it is an anti-inflammatory and therapeutic resinous substance. This study aimed to enhance the biological features of propolis extract by loading it onto active film. Firstly, extraction was performed using three solvent systems, and their total phenolic, flavonoid, and antioxidant activity was measured. Propolis ethanol extract (EEP) was evaluated for phenolic fraction content and then chosen to prepare a chitosan-loaded emulsion with several concentrations. The antibacterial, anti-mycotic, and anti-mycotoxigenic properties of the extract and nanoemulsion were assessed. PPE's cytotoxicity and nanoemulsion were evaluated using brine shrimp and cell line assays. Results indicate higher phenolic (322.57 ± 4.28 mg GAE/g DW), flavonoid (257.64 ± 5.27 mg QE/g DW), and antioxidant activity of the EEP. The phenolic fraction is distinguished by 18 phenolic acids with high p-hydroxybenzoic content (171.75 ± 1.64 µg/g) and 12 flavonoid compounds with high pinocembrin and quercetin content (695.91 ± 1.76 and 532.35 ± 1.88 µg/g, respectively). Phenolic acid derivatives (3,4-Dihydroxybenzaldehyde, 3,4-Dihydroxyphenol acetate, and di-methoxy cinnamic) are also found. Concentrations of 50, 100, 150, and 200 ng EEP loaded on chitosan nanoemulsion reflect significant antibacterial activity against pathogenic bacteria, particularly methicillin-resistant Staphylococcus aureus (MRSA) and toxigenic fungi, particularly Fusarium. Among the four EEP-loaded concentrations, the nanoemulsion with 150 ng showed outstanding features. Using a simulated medium, 150 and 200 ng of EEP-loaded chitosan nanoemulsion concentrations can stop zearalenone production in Fusarium media with complete fungi inhibition. Also, it reduced aflatoxins production in Aspergillus media, with fungal inhibition (up to 47.18%). These results recommended the EEP-chitosan application for pharmaceutics and medical use as a comprehensive wound healing agent.

Carbapenem resistance in Enterobacterales from agricultural, environmental and clinical origins: South Africa in a global context

Carbapenem agents are regarded as last-resort antibiotics, however, bacterial resistance towards carbapenems has been reported in both clinical and agricultural settings worldwide. Carbapenem resistance, defined as the resistance of a bacteria towards one or more carbapenem drugs, can be mediated in either of, or a combination of, three mechanisms-although, the mechanism mediated through the production of carbapenemases (β-lactamases that are able to enzymatically degrade carbapenems) is of most significance. Of particular concern is the occurrence of carbapenemase producing Enterobacterales (CPE), with literature describing a dramatic increase in resistance globally. In South Africa, increases of carbapenemase activity occurring in Enterobacter species, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa have recently been reported. CPE can also be found in agricultural environments, as global studies have documented numerous instances of CPE presence in various animals such as pigs, cattle, seafood, horses and dogs. However, most reports of CPE occurrence in agricultural settings come from Northern America, Europe and some parts of Asia, where more extensive research has been conducted to understand the CPE phenomenon. In comparison to clinical data, there are limited studies investigating the spread of CPE in agricultural settings in Africa, highlighting the importance of monitoring CPE in livestock environments and the food chain. Further research is necessary to uncover the true extent of CPE dissemination in South Africa. This review will discuss the phenomenon of bacterial antibiotic resistance (ABR), the applications of the carbapenem drug and the occurrence of carbapenem resistance globally.

Assessing the mechanisms of multi-drug resistant non-typhoidal Salmonella (NTS) serovars isolated from layer chicken farms in Nigeria

BACKGROUND

In Nigeria, there have been reports of widespread multiple antimicrobial resistance (AMR) amongst Salmonella isolated from poultry. To mitigate the impact of mortality associated with Salmonella on their farms, farmers resort to the use of antimicrobials without sound diagnostic advice. We conducted this study to describe the AMR patterns, mechanisms and genetic similarities within some Salmonella serovars isolated from different layer farms.

METHOD

We determine the AMR profiles of two hundred Salmonella isolates, selected based on frequency, serovar, and geographical and sample type distribution. We also assessed the mechanisms of multi-drug resistance for specific genetic determinants by using PCR protocols and gene sequence analysis. Pulsed-field gel electrophoresis (PFGE) was conducted on seven selected serovars to determine their genetic relatedness.

RESULTS

Of 200 isolates, 97 (48.5%) revealed various AMR profiles, with the multiple antibiotic resistance (MAR) index ranging from 0.07-0.5. Resistance to ciprofloxacin was common in all the multi-drug resistant isolates, while all the isolates were susceptible to cefotaxime, ceftazidime, and meropenem. Genotypic characterization showed the presence of resistance genes as well as mutations in the nucleotide genes with subsequent amino acid substitutions. Fifteen isolates (43%) of S. Kentucky were indistinguishable, but were isolated from four different states in Nigeria (Ogun, n = 9; Kaduna, n = 6; Plateau, n = 3, and: Bauchi, n = 2). PFGE revealed 40 pulsotype patterns (Kentucky, n = 12; Larochelle, n = 9; Virchow, n = 5; Saintpaul, n = 4; Poona, n = 3; Isangi, n = 2, and; Nigeria, n = 2).

CONCLUSION

This study recorded strictly related but diversely distributed Salmonella serovars with high AMR rates in poultry. We recommend strict regulation on antimicrobial use and regular monitoring of AMR trends among bacteria isolated from animals and humans to inform public policy.

Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens

Antibiotic resistance is a growing threat to human health, caused in part by pathogens accumulating antibiotic resistance genes (ARGs) through horizontal gene transfer. New ARGs are typically not recognized until they have become widely disseminated, which limits our ability to reduce their spread. In this study, we use large-scale computational screening of bacterial genomes to identify previously undiscovered mobile ARGs in pathogens. From ~1 million genomes, we predict 1,071,815 genes encoding 34,053 unique aminoglycoside-modifying enzymes (AMEs). These cluster into 7,612 families (<70% amino acid identity) of which 88 are previously described. Fifty new AME families are associated with mobile genetic elements and pathogenic hosts. From these, 24 of 28 experimentally tested AMEs confer resistance to aminoglycoside(s) in Escherichia coli, with 17 providing resistance above clinical breakpoints. This study greatly expands the range of clinically relevant aminoglycoside resistance determinants and demonstrates that computational methods enable early discovery of potentially emerging ARGs.

Collateral sensitivity: An evolutionary trade-off between antibiotic resistance mechanisms, attractive for dealing with drug-resistance crisis

Background

The discovery and development of antimicrobial drugs were one of the most significant advances in medicine, but the evolution of microbial resistance limited the efficiency of these drugs.

Aim

This paper reviews the collateral sensitivity in bacteria and its potential and limitation as a new target for treating infections.

Results and Discussion

Knowledge mechanisms of resistance to antimicrobial agents are useful to trace a practical approach to treat and control of resistant pathogens. The effect of a resistance mechanism to certain antibiotics on the susceptibility or resistance to other drugs is a key point that may be helpful for applying a strategy to control resistance challenges. In an evolutionary trade-off known as collateral sensitivity, the resistance mechanism to a certain drug may be mediated by the hypersensitivity to other drugs. Collateral sensitivity has been described for different drugs in various bacteria, but the molecular mechanisms affecting susceptibility are not well demonstrated. Collateral sensitivity could be studied to detect its potential in the battle against resistance crisis as well as in the treatment of pathogens adapting to antibiotics. Collateral sensitivity-based antimicrobial therapy may have the potential to limit the emergence of antibiotic resistance.

Molecular characterization and antibiotic resistance profile of ESBL-producing Escherichia coli isolated from healthy cow raw milk in smallholder dairy farms in Bangladesh

Background and Aim

The emergence of antimicrobial-resistant bacteria, such as Escherichia coli in milk, is a serious public health concern as milk is considered a complete food and an important part of daily human diet worldwide, including in Bangladesh. However, there have been no reports on the molecular characterization and antibiotic resistance profile of extended-spectrum beta-lactamase (ESBL)-producing E. coli from milk of healthy cows in Bangladesh. Therefore, this study aimed to detect and characterize ESBL-producing E. coli (ESBL-Ec) in milk samples from healthy cows in smallholder dairy farms in Mymensingh district, Bangladesh, and assess the potential risk of consuming this milk.

Materials and Methods

A total of 100 milk samples were collected from apparently healthy cows on smallholder dairy farms. Escherichia coli was isolated from the collected samples using standard methods. The detection of ESBL-Ec was performed phenotypically using cultural methods and genotypically by ESBL genetic determinants using multiplex polymerase chain reaction. Antimicrobial susceptibility testing of the ESBL-Ec isolates was performed using the disk diffusion method with 15 common antimicrobials.

Results

In this study, out of the 100 samples tested, 70 (70%) were found to be positive for E. coli. Among these, 41 (58.6%) strains were identified as ESBL-producing, both phenotypically and genotypically, with the presence of blaCTX-M, blaTEM, and blaSHV individually or combined (blaCTX-M plus blaTEM plus blaSHV). The antibiogram of these ESBL-positive isolates revealed high resistance against commonly used antibiotics, such as ampicillin, cefotaxime, and gentamicin (100%), azithromycin (88%), oxytetracycline (27%), nalidixic acid, cotrimoxazole/trimethoprim (24%), and streptomycin (22%). In addition, one isolate showed resistance to 4th generation of cephalosporin (cefepime). Most importantly, extensive multidrug resistance was found in many ESBL-Ec isolates. However, the isolates were highly sensitive to drugs such as ceftriaxone (100%) and imipenem (100%). This is the first study to detect ESBL-Ec in raw milk from healthy cows on smallholder dairy farms in Bangladesh.

Conclusion

More than 58% of the E. coli isolated from raw milk of healthy cows tested positive for ESBL production and showed resistance to most commonly used antimicrobials which may be alarming for human health. A limitation of our study is that we had a small size of sample collected from one district in Bangladesh. Therefore, a larger sample size covering a wider geographic area, and using multi-locus sequence typing and whole genome sequencing could provide a more comprehensive understanding of the prevalence and characteristics of ESBL-Ec in Bangladesh.

Efflux Pump Inhibitors in Controlling Antibiotic Resistance: Outlook under a Heavy Metal Contamination Context

Multi-drug resistance to antibiotics represents a growing challenge in treating infectious diseases. Outside the hospital, bacteria with the multi-drug resistance (MDR) phenotype have an increased prevalence in anthropized environments, thus implying that chemical stresses, such as metals, hydrocarbons, organic compounds, etc., are the source of such resistance. There is a developing hypothesis regarding the role of metal contamination in terrestrial and aquatic environments as a selective agent in the proliferation of antibiotic resistance caused by the co-selection of antibiotic and metal resistance genes carried by transmissible plasmids and/or associated with transposons. Efflux pumps are also known to be involved in either antibiotic or metal resistance. In order to deal with these situations, microorganisms use an effective strategy that includes a range of expressions based on biochemical and genetic mechanisms. The data from numerous studies suggest that heavy metal contamination could affect the dissemination of antibiotic-resistant genes. Environmental pollution caused by anthropogenic activities could lead to mutagenesis based on the synergy between antibiotic efficacy and the acquired resistance mechanism under stressors. Moreover, the acquired resistance includes plasmid-encoded specific efflux pumps. Soil microbiomes have been reported as reservoirs of resistance genes that are available for exchange with pathogenic bacteria. Importantly, metal-contaminated soil is a selective agent that proliferates antibiotic resistance through efflux pumps. Thus, the use of multi-drug efflux pump inhibitors (EPIs) originating from natural plants or synthetic compounds is a promising approach for restoring the efficacy of existing antibiotics, even though they face a lot of challenges.

The rise of multidrug resistant Salmonella isolates in healthy chickens in Brazil by successful establishment of plasmid IncHI2A carrying several antibiotic resistance genes

Salmonella spp. is an important global issue in food-producing animals. The present study evaluated antimicrobial resistance and virulence profiles in Salmonella spp. isolates from chickens in Brazil. Identification of serotypes, virulence and antimicrobial resistance genes, and plasmid profiles were performed. Three different serovars were found, S. Schwarzengrund, S. Newport and S. Kentucky. All isolates were considered Multidrug- resistance (MDR). Among the 32 Salmonella spp. isolates analysed, 29 isolates carried blaCTX-M-2 gene and showed the insertion sequence ISCR1 and a class 1 integron structure upstream from blaCTX-M-2. This gene was harboured in large IncHI2A plasmids with approximately 280kb. Furthermore, 30 isolates harboured tetA and tetB genes and 25 also harboured qnrB. The virulence genes invA, misL, orfL, spiC and pipD were detected in all isolates. The study shows a high prevalence of MDR Salmonella isolates disseminated in poultry farms. The association of the replicon IncHI2A with the resistance genes found, elevate the risk of foodborne disease outbreaks.

Antimicrobial resistance pattern of avian pathogenic Escherichia coli with detection of extended-spectrum β-lactamase-producing isolates in broilers in east Algeria

Background and Aim: Avian pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis, one of the most prevalent bacterial diseases responsible for significant economic losses in the poultry industry worldwide. This study aimed to assess the antimicrobial resistance (AMR) patterns of APEC isolates recovered from poultry in east Algeria and estimate the prevalence of extended-spectrum β-lactamase (ESBL)-producing isolates. Materials and Methods: In the slaughterhouse of Batna City (Algeria), livers indicating colibacillosis were sampled from 204 suspected carcasses with growth retardation and generalized congestion. Escherichia coli isolation and identification were performed on MacConkey agar using conventional methods and the API 20E system. Antimicrobial resistance susceptibility was tested by the disk diffusion method according to the Clinical Laboratory Standards Institute Guidelines. Extended-spectrum β-lactamase detection was carried out using the double-disk confirmation test. Results: One hundred sixty E. coli isolates were recovered (one isolate per sample). Avian pathogenic Escherichia coli isolates showed high levels of resistance to ampicillin and tetracycline (100%), nalidixic acid (95%), ofloxacin (93.75%), doxycycline (91.87), ciprofloxacin (87.50%), trimethoprim/sulfamethoxazole (62.50%), gentamycin (32.50%), chloramphenicol (27.50%), amoxicillin/clavulanic acid (16.25%), colistin (14.37%), and nitrofurantoin (10.62%). All strains were multidrug-resistant to at least three antibiotics, and more than half (52.52%) of the isolates were resistant to at least seven antibiotics. All isolates were susceptible to ceftriaxone, ceftazidime, and aztreonam. Two E. coli isolates were ESBL producers (1.25%). Conclusion: Avian pathogenic Escherichia coli resistance to most antimicrobial agents used in poultry may lead to antimicrobial therapy failure. Keywords: antimicrobial resistance, avian pathogenic Escherichia coli, broilers, colibacillosis, Eastern Algeria, extended-spectrum β-lactamase.

The effect of disinfectants and antiseptics on co- and cross-selection of resistance to antibiotics in aquatic environments and wastewater treatment plants

The outbreak of the SARS-CoV-2 pandemic led to increased use of disinfectants and antiseptics (DAs), resulting in higher concentrations of these compounds in wastewaters, wastewater treatment plant (WWTP) effluents and receiving water bodies. Their constant presence in water bodies may lead to development and acquisition of resistance against the DAs. In addition, they may also promote antibiotic resistance (AR) due to cross- and co-selection of AR among bacteria that are exposed to the DAs, which is a highly important issue with regards to human and environmental health. This review addresses this issue and provides an overview of DAs structure together with their modes of action against microorganisms. Relevant examples of the most effective treatment techniques to increase the DAs removal efficiency from wastewater are discussed. Moreover, insight on the resistance mechanisms to DAs and the mechanism of DAs enhancement of cross- and co-selection of ARs are presented. Furthermore, this review discusses the impact of DAs on resistance against antibiotics, the occurrence of DAs in aquatic systems, and DA removal mechanisms in WWTPs, which in principle serve as the final barrier before releasing these compounds into the receiving environment. By recognition of important research gaps, research needs to determine the impact of the majority of DAs in WWTPs and the consequences of their presence and spread of antibiotic resistance were identified.

Bioavailability of potentially toxic elements influences antibiotic resistance gene and mobile genetic element abundances in urban and rural soils

Antibiotic resistance genes (ARGs) that can encode resistance traits in bacteria are found across the environment. While it is often difficult to discern their origin, their prevalence and diversity depends on many factors, one of which is their exposure to potentially toxic elements (PTE, i.e., metals and metalloids) in soils. Here, we investigated how ambient ARGs and mobile genetic elements (MGEs) relate to the relative bioavailability of different PTEs (total versus exchangeable and carbonate-bound PTE) in rural and urban soils in northeast England. The average relative abundances of ARGs in rural sites varied over a 3-log range (7.24 × 10^-7 to 1.0 × 10^-4 genes/16S rRNA), and relative ARG abundances in urban sites varied by four orders of magnitude (1.75 × 10^-6 to 2.85 × 10^-2 genes/16S rRNA). While beta-lactam and aminoglycoside resistance genes dominated rural and urban sites, respectively, non-specific ARGs, also called multidrug-resistance genes, were significantly more abundant in urban sites (p < 0.05). Urban sites also had higher concentrations of total and exchangeable forms of PTE than rural sites, whereas rural sites were higher in carbonate-bound forms. Significant positive Spearman correlations between PTEs, ARGs and MGEs were apparent, especially with bioavailable PTE fractions and at urban sites. This study found significant positive correlations between ARGs and beryllium (Be), which has not previously been reported. Overall, our results show that PTE bioavailability is important in explaining the relative selection of ARGs in soil settings and must be considered in future co-selection and ARG exposure studies.

Relevance of the Consensus Principles for Appropriate Antibiotic Prescribing in 2022

Background

In the late 1990s, as a response to rising antimicrobial resistance (AMR), an independent multinational, interdisciplinary group was formed specifically targeting primary care antibiotic prescribing for community-acquired respiratory tract infections (CA-RTIs). The group comprised senior clinicians from Canada, Israel, Spain, Sweden, UK and USA. The group’s objectives were to provide recommendations for antibiotic stewardship in the community because, whilst it was widely accepted that inappropriate antibiotic use was contributing to AMR, it remained difficult to change prescribing behaviour. The group aimed to identify principles underlying appropriate antibiotic prescribing and guideline formulation to reduce morbidity from CA-RTIs, limit therapeutic failure and, importantly, curb AMR emergence. The group published a report in 2002, which has become known as the Consensus Principles.

Objectives

(i) To consider the relevance of the Consensus Principles in 2022 by reviewing current global approaches to rising AMR. A wide range of factors, such as antibiotic overuse, most recently seen in COVID-19 patients, are still driving rising AMR even though there has been a high-level international response to the AMR threat; and (ii) as an introduction to this Supplement, which reports the findings of analyses of how AMR is being addressed in nine disparate countries (Brazil, India, Kuwait, Mexico, Pakistan, Russia, Saudi Arabia, Türkiye and Vietnam). Understanding how these initiatives are being pursued in different countries helps identify areas where more information is needed.

Conclusions

Adherence to the Consensus Principles remains as important now as it was in 2002. Achieving appropriate antibiotic prescribing is a vital objective in order that the right patient receives the right antibiotics at the right time to ensure optimal clinical outcomes while at the same time helping to limit further increases in AMR.

Identifying patient-level risk factors associated with non-β-lactam resistance outcomes in invasive MRSA infections in the United States using chain graphs

Background

MRSA is one of the most common causes of hospital- and community-acquired infections. MRSA is resistant to many antibiotics, including β-lactam antibiotics, fluoroquinolones, lincosamides, macrolides, aminoglycosides, tetracyclines and chloramphenicol.

Objectives

To identify patient-level characteristics that may be associated with phenotype variations and that may help improve prescribing practice and antimicrobial stewardship.

Methods

Chain graphs for resistance phenotypes were learned from invasive MRSA surveillance data collected by the CDC as part of the Emerging Infections Program to identify patient level risk factors for individual resistance outcomes reported as MIC while accounting for the correlations among the resistance traits. These chain graphs are multilevel probabilistic graphical models (PGMs) that can be used to quantify and visualize the complex associations among multiple resistance outcomes and their explanatory variables.

Results

Some phenotypic resistances had low connectivity to other outcomes or predictors (e.g. tetracycline, vancomycin, doxycycline and rifampicin). Only levofloxacin susceptibility was associated with healthcare-associated infections. Blood culture was the most common predictor of MIC. Patients with positive blood culture had significantly increased MIC of chloramphenicol, erythromycin, gentamicin, lincomycin and mupirocin, and decreased daptomycin and rifampicin MICs. Some regional variations were also observed.

Conclusions

The differences in resistance phenotypes between patients with previous healthcare use or positive blood cultures, or from different states, may be useful to inform first-choice antibiotics to treat clinical MRSA cases. Additionally, we demonstrated multilevel PGMs are useful to quantify and visualize interactions among multiple resistance outcomes and their explanatory variables.

Resistance mechanisms in Gram-negative bacteria

Enterobacterales resistant to carbapenems or producing extended-spectrum β-lactamases (ESBL) and non-fermenters resistant to carbapenems present resistance to many of the antimicrobials commonly used in clinical practice, and have been recognized by the World Health Organization as a critical priority for the development of new antimicrobials. In this review, the main mechanisms of resistance of Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia to β-lactams, quinolones, aminoglycosides and polymyxins will be addressed. Updated information will be presented on the importance in resistance of antimicrobial modification mechanisms (including class C or extended-spectrum β-lactamases, carbapenemases and aminoglycoside-modifying enzymes), permeability alterations due to porin or lipopolysaccharide expression disorders, production of active efflux pumps, target alterations or protection, and expression of two-component systems.

Uses of mathematical modeling to estimate the impact of mass drug administration of antibiotics on antimicrobial resistance within and between communities

Background

Antibiotics are a key part of modern healthcare, but their use has downsides, including selecting for antibiotic resistance, both in the individuals treated with antibiotics and in the community at large. When evaluating the benefits and costs of mass administration of azithromycin to reduce childhood mortality, effects of antibiotic use on antibiotic resistance are important but difficult to measure, especially when evaluating resistance that “spills over” from antibiotic-treated individuals to other members of their community. The aim of this scoping review was to identify how the existing literature on antibiotic resistance modeling could be better leveraged to understand the effect of mass drug administration (MDA) on antibiotic resistance.

Main text

Mathematical models of antibiotic use and resistance may be useful for estimating the expected effects of different MDA implementations on different populations, as well as aiding interpretation of existing data and guiding future experimental design. Here, strengths and limitations of models of antibiotic resistance are reviewed, and possible applications of those models in the context of mass drug administration with azithromycin are discussed.

Conclusions

Statistical models of antibiotic use and resistance may provide robust and relevant estimates of the possible effects of MDA on resistance. Mechanistic models of resistance, while able to more precisely estimate the effects of different implementations of MDA on resistance, may require more data from MDA trials to be accurately parameterized.

Graphical Abstract

Metaphylactic antimicrobial effects on occurrences of antimicrobial resistance in Salmonella, Escherichia coli, and Enterococcus spp. measured longitudinally from feedlot arrival to harvest in high-risk beef cattle

Aims

Our objective was to determine how injectable antimicrobials affected populations of Salmonella enterica, Escherichia coli and Enterococcus spp. in feedlot cattle.

Methods and Results

Two arrival date blocks of high‐risk crossbred beef cattle (n = 249; mean BW = 244 kg) were randomly assigned one of four antimicrobial treatments administered on day 0: sterile saline control (CON), tulathromycin (TUL), ceftiofur (CEF) or florfenicol (FLR). Faecal samples were collected on days 0, 28, 56, 112, 182 and study end (day 252 for block 1 and day 242 for block 2). Hide swabs and subiliac lymph nodes were collected the day before and the day of harvest. Samples were cultured for antimicrobial‐resistant Salmonella, Escherichia coli and Enterococcus spp. The effect of treatment varied by day across all targeted bacterial populations (p ≤ 0.01) except total E. coli. Total E. coli counts were greatest on days 112, 182 and study end (p ≤ 0.01). Tulathromycin resulted in greater counts and prevalence of Salmonella from faeces than CON at study end (p ≤ 0.01). Tulathromycin and CEF yielded greater Salmonella hide prevalence and greater counts of 128ERY^RE. coli at study end than CON (p ≤ 0.01). No faecal Salmonella resistant to tetracyclines or third‐generation cephalosporins were detected. Ceftiofur was associated with greater counts of 8ERY^REnterococcus spp. at study end (p ≤ 0.03). By the day before harvest, antimicrobial use did not increase prevalence or counts for all other bacterial populations compared with CON (p ≥ 0.13).

Conclusions

Antimicrobial resistance (AMR) in feedlot cattle is not caused solely by using a metaphylactic antimicrobial on arrival, but more likely a multitude of environmental and management factors.

Potent Activity of a High Concentration of Chemical Ozone against Antibiotic-Resistant Bacteria

BACKGROUND

Health care-associated infections (HAIs) are a significant public health problem worldwide, favoring multidrug-resistant (MDR) microorganisms. The SARS-CoV-2 infection was negatively associated with the increase in antimicrobial resistance, and the ESKAPE group had the most significant impact on HAIs. The study evaluated the bactericidal effect of a high concentration of O3 gas on some reference and ESKAPE bacteria.

MATERIAL AND METHODS

Four standard strains and four clinical or environmental MDR strains were exposed to elevated ozone doses at different concentrations and times. Bacterial inactivation (growth and cultivability) was investigated using colony counts and resazurin as metabolic indicators. Scanning electron microscopy (SEM) was performed.

RESULTS

The culture exposure to a high level of O3 inhibited the growth of all bacterial strains tested with a statistically significant reduction in colony count compared to the control group. The cell viability of S. aureus (MRSA) (99.6%) and P. aeruginosa (XDR) (29.2%) was reduced considerably, and SEM showed damage to bacteria after O3 treatment Conclusion: The impact of HAIs can be easily dampened by the widespread use of ozone in ICUs. This product usually degrades into molecular oxygen and has a low toxicity compared to other sanitization products. However, high doses of ozone were able to interfere with the growth of all strains studied, evidencing that ozone-based decontamination approaches may represent the future of hospital cleaning methods.

Global Distribution of Extended Spectrum Cephalosporin and Carbapenem Resistance and Associated Resistance Markers in Escherichia coli of Swine Origin - A Systematic Review and Meta-Analysis

Third generation cephalosporins and carbapenems are considered critically important antimicrobials in human medicine. Food animals such as swine can act as reservoirs of antimicrobial resistance (AMR) genes/bacteria resistant to these antimicrobial classes, and potential dissemination of AMR genes or resistant bacteria from pigs to humans is an ongoing public health threat. The objectives of this systematic review and meta-analysis were to: (1) estimate global proportion and animal-level prevalence of swine E. coli phenotypically resistant to third generation cephalosporins (3GCs) and carbapenems at a country level; and (2) measure abundances and global distribution of the genetic mechanisms that confer resistance to these antimicrobial classes in these E. coli isolates. Articles from four databases (CAB Abstracts, PubMed/MEDLINE, PubAg, and Web of Science) were screened to extract relevant data. Overall, proportion of E. coli resistant to 3GCs was lower in Australia, Europe, and North America compared to Asian countries. Globally, <5% of all E. coli were carbapenem-resistant. Fecal carriage rates (animal-level prevalence) were consistently manifold higher as compared to pooled proportion of resistance in E. coli isolates. bla_CTX–M were the most common 3GC resistance genes globally, with the exception of North America where bla_CMY were the predominant 3GC resistance genes. There was not a single dominant bla_CTX–M gene subtype globally and several bla_CTX–M subtypes were dominant depending on the continent. A wide variety of carbapenem-resistance genes (bla_{NDM–, VIM–, IMP–, OXA–48}, _andKPC–) were identified to be circulating in pig populations globally, albeit at very-low frequencies. However, great statistical heterogeneity and a critical lack of metadata hinders the true estimation of prevalence of phenotypic and genotypic resistance to these antimicrobials. Comparatively frequent occurrence of 3GC resistance and emergence of carbapenem resistance in certain countries underline the urgent need for improved AMR surveillance in swine production systems in these countries.

Integrated meta-omics study on rapid tylosin removal mechanism and dynamics of antibiotic resistance genes during aerobic thermophilic fermentation of tylosin mycelial dregs

For efficient treatment of tylosin mycelial dregs (TMDs), rapid tylosin removal mechanism and dynamics of ARGs during TMDs fermentation were investigated using integrated meta-omics (genomics, metaproteomics and metabolomics) and qPCR approaches. The results showed that over 86% of tylosin was degraded on day 7 regardless of the type of bulking agents. The rapid removal of tylosin was mainly attributed to de-mycarose reaction (GH3) and esterase hydrolysis (C7MYQ7) of Saccharomonospora, and catalase-peroxidase oxidation of Bacillus (A0A077JB13). In addition, the moisture content and mobile genetic elements were vital to control the rebound of ARGs. The removal efficiency of antibiotic resistant bacteria (Streptomyces, Pseudomonas, norank_f__Sphingobacteriaceae, and Paenalcaligenes) and Intl1 (98.8%) in fermentation treatment TC21 with corncob as the bulking agent was significantly higher than that in other three treatments (88.3%). Thus, appropriate bulking agents could constrain the abundance of antibiotic resistant bacteria and Intl1, which is crucial to effectively reduce the resistance.

Prevalence of Antimicrobial Resistant and Extended-Spectrum Beta-Lactamase-producing Escherichia coli in Dairy Cattle Farms in East Tennessee

Antimicrobials have been widely used in dairy farms to prevent and control dairy cattle diseases since 1960s. This led to the emergence of antimicrobial resistant bacteria (ARB) that, along with their antimicrobial resistance genes (ARGs), can spread from dairy farms to humans. Therefore, regular antimicrobial resistance (AMR) monitoring is important to implement proper mitigation measures. The objective of this study was to determine the prevalence of AMR and extended-spectrum beta-lactamases (ESBLs)-producing Escherichia coli in dairy cattle. A cross-sectional study was conducted in four dairy cattle farms (A-D) in East Tennessee. A total of 80 samples consisting of 20 samples each of bulk tank milk, feces, dairy cattle manure-amended soil, and prairie soil adjacent to the farms were collected and cultured for the isolation of E. coli. Tetracycline (TET^r)-, third-generation cephalosporin (TGC^r)- and nalidixic acid (NAL^r)-resistant E. coli (n = 88) were isolated and identified on agar media supplemented with TET, cefotaxime, and NAL, respectively. TGC^r E. coli were tested for ESBLs and other coselected ARGs. TET^r (74%, n = 88) was the most common, followed by TGC^r (20%) and NAL^r (8%). Farms had significant (p < 0.001) differences: the highest prevalence of TGC^r (55%) and TET^r (100%) were observed in farm D, while all NAL^r isolates were from farm C. Over 83% of TGC^r isolates (n = 18) harbored ESBL gene bla_CTX-M. Majority (78%) of the E. coli isolates were multidrug-resistant (MDR), being positive for beta-lactams (bla_CTX-M), TETs tet(A), tet(B), tet(M)), sulfonamides (sul2), aminoglycosides (strA), and phenicols (floR). This study indicated the widespread occurrence of MDR ESBLs-E. coli in dairy cattle farms. AMR surveillance of more dairy farms and identification of farm-level risk factors are important to mitigate the occurrence and spread of ARB of significant public health importance, such as ESBLs-E. coli.

Global Distribution of Fluoroquinolone and Colistin Resistance and Associated Resistance Markers in Escherichia coli of Swine Origin - A Systematic Review and Meta-Analysis

Background

Fluoroquinolones and polymyxins (colistin) are considered as critical drugs for human medicine. Antimicrobials of these classes are also used in swine production worldwide and this usage can contribute to selection of antimicrobial resistance (AMR), which is a threat to both human and animal health. Given the dynamic epidemiology of AMR, updating our knowledge regarding distribution and trends in the proportion of resistant bacteria is of critical importance.

Objectives

The aim of this systematic review and meta-analysis was to describe the global prevalence of phenotypic and genotypic resistance to fluoroquinolones and colistin in Escherichia coli collected from swine.

Results

Four databases (PubMed, PubAg, Web of Science, and CAB abstracts) and reports of national surveillance programs were scanned and 360 articles were included in the analysis. We identified higher prevalence levels of fluoroquinolone and colistin resistance in isolates from pig populations in Asia compared to Europe. The heterogeneity of pooled estimates was also higher in Asian countries suggesting that prevalence of AMR is still not fully characterized. There was a major knowledge gap about the situation of AMR in South American and African countries. We also identified key deficiencies in how AMR data was reported in the studies. A meta-analysis using 6,167 publicly available genomes of swine E. coli established the prevalence and global distribution of genetic determinants that can lead to fluoroquinolone and colistin resistance.

Conclusion

This study provides the most comprehensive information on prevalence of phenotypic and genotypic resistance to key antimicrobials in pig populations globally. There is a need to establish national surveillance programs and effective policies, particularly in certain world regions, to curtail the threat of evolution of resistant isolates in swine production that can potentially contribute to public health detrimentally.

Diversity of blaCTX-M-1-carrying plasmids recovered from Escherichia coli isolated from Canadian domestic animals

Conserved IncI1 and IncHI1 plasmids carrying blaCTX-M-1 have been found circulating in chickens and horses from continental Europe, respectively. In Canada, blaCTX-M-1 is overwhelmingly the most common blaCTX-M variant found in Escherichia coli from chicken and horses and can be recovered at lower frequencies in swine, cattle, and dogs. Whole-genome sequencing has identified a large genetic diversity of isolates carrying this variant, warranting further investigations into the plasmids carrying this gene. Therefore, the objective of this study was to describe the genetic profiles of blaCTX-M-1 plasmids circulating in E. coli from Canadian domestic animals and compare them to those recovered in animals in Europe. Fifty-one blaCTX-M-1 positive E. coli isolates from chicken (n = 14), horses (racetrack horses n = 11; community horses n = 3), swine (n = 7), turkey (n = 6), dogs (n = 5), beef cattle (n = 3), and dairy cattle (n = 2) were selected for plasmid characterization. Sequences were obtained through both Illumina and Oxford Nanopore technologies. Genomes were assembled using either Unicycler hybrid assembly or Flye with polishing performed using Pilon. blaCTX-M-1 was found residing on a plasmid in 45 isolates and chromosomally located in six isolates. A conserved IncI1/ST3 plasmid was identified among chicken (n = 12), turkey (n = 4), swine (n = 6), dog (n = 2), and beef cattle (n = 2) isolates. When compared against publicly available data, these plasmids showed a high degree of similarity to those identified in isolates from poultry and swine in Europe. These results suggest that an epidemic IncI1/ST3 plasmid similar to the one found in Europe is contributing to the spread of blaCTX-M-1 in Canada. A conserved IncHI1/FIA(HI1)/ST2 plasmid was also recovered from nearly all racetrack horse isolates (n = 10). Although IncHI1/ST2 plasmids have been reported among European horse isolates, IncHI1/ST9 plasmids appear to be more widespread. Further studies are necessary to understand the factors contributing to these plasmids' success in their respective populations.

Plethora of Resistance Genes in Carbapenem-Resistant Gram-Negative Bacteria in Greece: No End to a Continuous Genetic Evolution

Carbapenem-resistant Gram-negative bacteria are a public health threat that requires urgent action. The fact that these pathogens commonly also harbor resistance mechanisms for several other antimicrobial classes further reduces patient treatment options. The present study aimed to provide information regarding the multidrug resistance genetic background of carbapenem-resistant Gram-negative bacteria in Central Greece. Strains from a tertiary care hospital, collected during routine practice, were characterized using a DNA microarray-based assay. Various different resistance determinants for carbapenems, other beta-lactams, aminoglycosides, quinolones, trimethoprim, sulfonamides and macrolides were detected among isolates of the same sequence type. Eighteen different multidrug resistance genomic profiles were identified among the twenty-four K. pneumoniae ST258, seven different profiles among the eight K. pneumoniae ST11, four profiles among the six A. baumannii ST409 and two among the three K. oxytoca. This report describes the multidrug resistance genomic background of carbapenem-resistant Gram-negative bacteria from a tertiary care hospital in Central Greece, providing evidence of their continuous genetic evolution.

Antimicrobial Stewardship Program: Reducing Antibiotic's Spectrum of Activity Is not the Solution to Limit the Emergence of Multidrug-Resistant Bacteria

Overconsumption of antibiotics in hospitals has led to policy implementation, including the control of antibiotic prescriptions. The impact of these policies on the evolution of antimicrobial resistance remains uncertain. In this work, we review the possible limits of such policies and focus on the need for a more efficient approach. Establishing a causal relationship between the introduction of new antibiotics and the emergence of new resistance mechanisms is difficult. Several studies have demonstrated that many resistance mechanisms existed before the discovery of antibiotics. Overconsumption of antibiotics has worsened the phenomenon of resistance. Antibiotics are responsible for intestinal dysbiosis, which is suspected of being the source of bacterial resistance. The complexity of the intestinal microbiota composition, the impact of the pharmacokinetic properties of antibiotics, and the multiplicity of other factors involved in the acquisition and emergence of multidrug-resistant organisms, lead us to think that de-escalation, in the absence of studies proving its effectiveness, is not the solution to limiting the spread of multidrug-resistant organisms. More studies are needed to clarify the ecological risk caused by different antibiotic classes. In the meantime, we need to concentrate our efforts on limiting antibiotic prescriptions to patients who really need it, and work on reducing the duration of these treatments.

Antimicrobial resistance bacteria and genes detected in hospital sewage provide valuable information in predicting clinical antimicrobial resistance

Extensive use of antibiotics is significantly associated with development of antibiotic-resistant (AR) bacteria. However, their causal relationships have not been adequately investigated, especially in human population and hospitals. Our aims were to understand clinical AR through revealing co-occurrence patterns between antibiotic-resistant bacteria and genes (ARB and ARGs), and their association with antibiotic use, and to consider impact of ARB and ARGs on environmental and human health. Antibiotic usage was calculated based on the actual consumption in our target hospital. ARB was identified by culture. In isolates collected from hospital sewage, bacterial-specific DNA sequences and ARGs were determined using metagenomics. Our data revealed that the use of culture-based single-indicator-strain approaches only captured ARB in 16.17% of the infectious samples. On the other hand, 1573 bacterial species and 885 types of ARGs were detected in the sewage. Furthermore, hospital use of antibiotics influenced the resistance profiles, but the strength varied among bacteria. From our metagenomics analyses, ARGs for aminoglycosides were the most common, followed by sulfonamide, tetracycline, phenicol, macrolides, and quinolones, comprising 82.6% of all ARGs. Association analyses indicated that 519 pairs of ARGs were significantly correlated with ARB species (r > 0.8). The co-occurrence patterns of bacteria-ARGs mirrored the AR in the clinic. In conclusion, our systematic investigation further emphasized that antibiotic usage in hospital significantly influenced the abundance and types of ARB and ARGs in dose- and time-dependent manners which, in turn, mirrored clinical AR. In addition, our data provide novel information on development of certain ARB with multiple antibiotic resistance. These ARB and ARGs from sewage can also be disseminated into the environment and communities to create health problems. Therefore, it would be helpful to use such data to develop improved predictive risk model of AR, to enhance effective use of antibiotics, and to reduce environmental pollution.

Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

BACKGROUND

The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.

RESULTS

We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter, Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and β-dispersion of ARGs, which were predominantly assigned to Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities started. ARGs associated with resistance to β-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.

CONCLUSIONS

The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility. Video Abstract.

OXA-48 Carbapenemase-Encoding Transferable Plasmids of Klebsiella pneumoniae Recovered from Egyptian Patients Suffering from Complicated Urinary Tract Infections

Gram-negative bacteria are common causes of urinary tract infections (UTIs). Such pathogens can acquire genes encoding multiple mechanisms of antimicrobial resistance, including carbapenem resistance. The aim of this study was to detect the carbapenemase-producing ability of some Gram-negative bacterial isolates from urine specimens of patients suffering from complicated UTIs at two vital tertiary care hospitals in Cairo, Egypt; to determine the prevalence of carbapenemase genes among plasmid-bearing isolates; and explore the possibility of horizontal gene transfer to other bacterial species. The collected isolates were subjected to antimicrobial susceptibility testing, phenotypic analysis of carbapenemase production, and molecular detection of plasmid-borne carbapenemase genes, then the extracted plasmids were transformed into competent E. coli DH5α. A total of 256 Gram-negative bacterial clinical isolates were collected, 65 (25.4%) isolates showed carbapenem resistance of which 36 (55.4%) were carbapenemase-producers, and of these 31 (47.7%) harbored plasmids. The extracted plasmids were used as templates for PCR amplification of bla_KPC, bla_NDM, bla_VIM, bla_OXA-48, and bla_IMP carbapenemase genes. The bla_OXA-48 gene was detected in 24 (77.4%) of the tested isolates while bla_VIM gene was detected in 8 (25.8%), both bla_KPC and bla_NDM genes were co-present in 1 (3.2%) isolate. Plasmids carrying the bla_OXA-48 gene from 4 K. pneumoniae clinical isolates were successfully transformed into competent E. coli DH5α. The transformants were carbapenemase-producers and acquired resistance to some of the tested antimicrobial agents as compared to untransformed E. coli DH5α. The study concluded that the rate of carbapenem resistance among Gram-negative bacterial uropathogens in Cairo, Egypt is relatively high and can be transferred horizontally to other bacterial host(s).

Genetic basis of molecular mechanisms in β-lactam resistant gram-negative bacteria

Antibiotic-resistant bacteria are considered one of the major global threats to human and animal health. The most harmful among the resistant bacteria are β-lactamase producing Gram-negative species (β-lactamases). β-lactamases constitute a paradigm shift in the evolution of antibiotic resistance. Therefore, it is imperative to present a comprehensive review of the mechanisms responsible for developing antimicrobial resistance. Resistance due to β-lactamases develops through a variety of mechanisms, and the number of resistant genes are involved that can be transferred between bacteria, mostly via plasmids. Over time, these new molecular-based resistance mechanisms have been progressively disclosed. The present review article provides information on the recent findings regarding the molecular mechanisms of resistance to β-lactams in Gram-negative bacteria, including CTX-M-type ESBLs with methylase activity, plasmids harbouring phages with β-lactam resistance genes, the co-presence of β-lactam resistant genes of unique combinations and the presence of β-lactam and non-β-lactam antibiotic-resistant genes in the same bacteria. Keeping in view, the molecular level resistance development, multifactorial and coordinated measures may be taken to counter the challenge of rapidly increasing β-lactam resistance.

Prevalence of antimicrobial resistance genes and its association with restricted antimicrobial use in food-producing animals: a systematic review and meta-analysis

BACKGROUND

There is ongoing debate regarding potential associations between restrictions of antimicrobial use and prevalence of antimicrobial resistance (AMR) in bacteria.

OBJECTIVES

To summarize the effects of interventions reducing antimicrobial use in food-producing animals on the prevalence of AMR genes (ARGs) in bacteria from animals and humans.

METHODS

We published a full systematic review of restrictions of antimicrobials in food-producing animals and their associations with AMR in bacteria. Herein, we focus on studies reporting on the association between restricted antimicrobial use and prevalence of ARGs. We used multilevel mixed-effects models and a semi-quantitative approach based on forest plots to summarize findings from studies.

RESULTS

A positive effect of intervention [reduction in prevalence or number of ARGs in group(s) with restricted antimicrobial use] was reported from 29 studies for at least one ARG. We detected significant associations between a ban on avoparcin and diminished presence of the vanA gene in samples from animals and humans, whereas for the mecA gene, studies agreed on a positive effect of intervention in samples only from animals. Comparisons involving mcr-1, blaCTX-M, aadA2, vat(E), sul2, dfrA5, dfrA13, tet(E) and tet(P) indicated a reduced prevalence of genes in intervention groups. Conversely, no effects were detected for β-lactamases other than blaCTX-M and the remaining tet genes.

CONCLUSIONS

The available body of scientific evidence supported that restricted use of antimicrobials in food animals was associated with an either lower or equal presence of ARGs in bacteria, with effects dependent on ARG, host species and restricted drug.

Low Proportion of Linezolid and Daptomycin Resistance Among Bloodborne Vancomycin-Resistant Enterococcus faecium and Methicillin-Resistant Staphylococcus aureus Infections in Europe

Vancomycin-resistant Enterococcus faecium (VREF) and methicillin-resistant Staphylococcus aureus (MRSA) are associated with significant health burden. We investigated linezolid and daptomycin resistance among VREF and MRSA in the EU/EEA between 2014 and 2018. Descriptive statistics and multivariable logistic regression were used to analyze 6,949 VREF and 35,131 MRSA blood isolates from patients with bloodstream infection. The population-weighted mean proportion of linezolid resistance in VREF and MRSA between 2014 and 2018 was 1.6% (95% CI 1.33–2.03%) and 0.28% (95% CI 0.32–0.38%), respectively. Daptomycin resistance in MRSA isolates was similarly low [1.1% (95% CI 0.75–1.6%)]. On the European level, there was no temporal change of daptomycin and linezolid resistance in MRSA and VREF. Multivariable regression analyses showed that there was a higher likelihood of linezolid and daptomycin resistance in MRSA (aOR: 2.74, p < 0.001; aOR: 2.25, p < 0.001) and linezolid in VREF (aOR: 1.99, p < 0.001) compared to their sensitive isolates. The low proportion of linezolid and daptomycin resistance in VREF and MRSA suggests that these last-resort antibiotics remain effective and will continue to play an important role in the clinical management of these infections in Europe. However, regional and national efforts to contain antimicrobial resistance should continue to monitor the trend through strengthened surveillance that includes genomic surveillance for early warning and action.

Trends in antimicrobial resistance amongst pathogens isolated from blood and cerebrospinal fluid cultures in Pakistan (2011-2015): A retrospective cross-sectional study

While antimicrobial resistance (AMR) continues to be a major public health problem in Pakistan, data regarding trends of resistance among pathogenic bacteria remains scarce, with few studies presenting long-term trends in AMR. This study was therefore designed to analyze long-term AMR trends at a national level in Pakistan. We report here results of a comprehensive analysis of resistance, among pathogens isolated from blood and cerebrospinal fluid (CSF), between 2011 and 2015. Susceptibility data was obtained from a local laboratory with collection points all across Pakistan (Chughtai Laboratory). Resistance proportions to most commonly used antimicrobials were calculated for each pathogen over a period of five years. While Acinetobacter species demonstrated highest resistance rates to all tested antimicrobials, a sharp increase in carbapenem resistance was the most noticeable (50%-95%) between 2011-2015. Our results also highlight the presence of third and fourth generation cephalosporins resistance in Salmonella enterica serovar Typhi in Pakistan. Interestingly, where rise in AMR was being observed in some major invasive pathogens, decreasing resistance trends were observed in Staphylococcus aureus, against commonly used antimicrobials. Overall pathogens isolated from blood and CSF between 2011-2015, showed an increase in resistance towards commonly used antimicrobials.

Green synthesized Silver Nanoparticles as Silver Lining in Antimicrobial Resistance: A Review

Unprincipled use of antibiotics has led to the antimicrobial resistance (AMR) against mostly available compounds and now become a major cause of concern for the scientific community. However, in the past decade, green synthesized silver nanoparticles (AgNPs) have received greater attention for the development of newer therapies as antimicrobials by virtue of their unique physico-chemical properties. Unlike traditional antibiotics, AgNPs exert their action by acting on multiple mechanisms which make them potential candidates against AMR. Green synthesis of AgNPs using various medicinal plants has demonstrated broader spectrum of action against several microbes in a number of attempts. The present paper provides an insight into the scientific studies that have elucidated the positive role of plant extracts/phytochemicals during green synthesis of AgNPs and their future perspectives. The studies conducted so far seem promising still, a few factors like, the precise mechanism of action of AgNPs, their synergistic interaction with biomolecules, and industrial scalability need to be explored further till effective drug development using green synthesized AgNPs in healthcare systems against AMR is established.

Resistance determinants and their genetic context in enterobacteria from a longitudinal study of pigs reared under various husbandry conditions

Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. Cefotaxime-resistant bacteria were quantified and isolated from feed, feces, manures and carcasses of pigs reared with penicillin-using or antibiotic-free husbandries. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays. The extended spectrum β-lactamase (ESBL) phenotype was more frequent in isolates originating from antibiotic-free animals, while the bacteria isolated from penicillin-using animals were on average resistant to a greater number of antibiotics. The ESBL-encoding genes identified were bla _CTX-M-1, bla _CTX-M-15 and bla _CMY-2 and they co-localised on plasmids with various genes encoding resistance to ß-lactams, co-trimoxazole, phenicols and tetracycline, all antibiotics used in pig production. Groups of genes conferring the observed resistance and the mobile elements disseminating multidrug resistance were determined. The observed resistance to ß-lactams was mainly due to the complementary actions of penicillin-binding proteins, an efflux pump and ß-lactamases. Most resistance determinants were shared by animals raised with or without antimicrobials. This suggests a key contribution of indigenous enterobacteria maternally transmitted along the sow lineage, regardless of antimicrobial use. It is unclear if the antimicrobial resistance observed in the enterobacteria populations of the commercial pig herds studied were present before the use of antibiotics, or the extent to which historical antimicrobial use exerted a selective pressure defining the resistant bacterial populations in farms using penicillin prophylaxis.Importance: Antimicrobial resistance is a global threat that needs to be fought on numerous fronts along the One Health continuum. Vast quantities of antimicrobials are used in agriculture to ensure animal welfare and productivity, and are arguably a driving force for the persistence of environmental and food-borne resistant bacteria. This study evaluated the impact of conventional, organic and other antibiotic-free husbandry practices on the frequency and nature of antimicrobial resistance genes and multidrug resistant enterobacteria. It provides knowledge about the relative contribution of specific resistance determinants to observed antibiotic resistance. It also showed the clear co-selection of genes coding for extended-spectrum beta-lactamases and genes coding for the resistance to antibiotics commonly used for prophylaxis or in curative treatments in pig operations.

Prevalence of mobile colistin resistance (mcr) genes in extended-spectrum β-lactamase-producing Escherichia coli isolated from retail raw foods in Nha Trang, Vietnam

The aim of the study was to assess the presence of genes in ESBL-producing E. coli (ESBL-Ec) isolated from retail raw food in Nha Trang, Vietnam. A total of 452 food samples comprising chicken (n = 116), pork (n = 112), fish (n = 112) and shrimp (n = 112) collected between 2015 and 2017 were examined for the prevalence of ESBL-Ec. ESBL-Ec were detected in 46.0% (208/452) of retail food samples, particularly in 66.4% (77/116), 55.4% (62/112), 42.0% (47/112) 19.6% (22/112) of chicken, pork, fish and shrimp, respectively. Sixty-five out of the 208 (31.3%) ESBL-Ec isolates were positive for mcr genes including mcr-1, mcr-3 and both mcr-1 and mcr-3 genes in 56/208 (26.9%), 1/208 (0.5%) and 8/208 (3.9%) isolates, respectively. Particularly, there was higher prevalence of mcr-1 in ESBL-Ec isolates from chicken (53.2%, 41/77) in comparison to shrimp (22.7%, 5/22), pork (11.3%, 7/62) and fish (6.4%, 3/47). mcr-3 gene was detected in co-existence with mcr-1 in ESBL-Ec isolates from shrimp (9.1%, 2/22), pork (8.1%, 5/62) and fish (2.1%, 1/47) but not chicken. The 65 mcr-positive ESBL-Ec (mcr-ESBL-Ec) were colistin-resistant with the MICs of 4-8 μg/mL. All mcr-3 gene-positive isolates belonged to group A, whereas phylogenetic group distribution of isolates harboring only mcr-1 was B1 (44.6%), A (28.6%) and D (26.8%). PFGE analysis showed diverse genotypes, although some isolates demonstrated nearly clonal relationships. S1-PFGE and Southern hybridization illustrated that the mcr-1 and mcr-3 genes were located either on chromosomes or on plasmids. However, the types of mcr genes were harbored on different plasmids with varied sizes of 30-390 kb. Besides, the ESBL genes of CTX-M-1 or CTX-M-9 were also detected to be located on plasmids. Noteworthy, co-location of CTX-M-1 with mcr-1 or mcr-3 genes on the same plasmid was identified. The conjugation experiment indicated that the mcr-1 or mcr-3 was horizontally transferable. All mcr-ESBL-Ec isolates were multidrug resistance (resistance to ≥3 antimicrobial classes). Moreover, β-Lactamase-encoding genes of the CTX-M-1 (78.5%), CTX-M-9 (21.5%), TEM (61.5%) groups were found in mcr-ESBL-Ec. The astA gene was detected in 27 (41.5%) mcr-ESBL-Ec isolates demonstrating their potential virulence. In conclusion, mcr-1 and mcr-3 genes existed individually or concurrently in ESBL-Ec isolates recovered from retail raw food in Nha Trang city, which might further complicate the antimicrobial-resistant situation in Vietnam, and is a possible health risk for human.

Occurrence of antibiotics and antibiotic resistance genes in the Fuxian Lake and antibiotic source analysis based on principal component analysis-multiple linear regression model

In recent years, the dramatic increase in antibiotic use has led to the evolution of antibiotic resistant genes (ARGs), posing a potential risk to human and aquatic ecological safety. In this study, source contribution and correlations between twelve antibiotics and their corresponding ARGs were firstly investigated in surface water in the Fuxian Lake. The results showed that sulfamethoxazole (SMX) (0.98-14.32 ng L^-1) and ofloxacin (OFL) (0.77-7.3 ng L^-1) were the dominant antibiotics in surface water, whereas erythromycin-H₂O (EM-H₂O), SMX and OFL posed the medium risk to aquatic organisms. Meanwhile, the mean concentrations of MLs in inflowing rivers were 5.6 times more than those in the lake, which was related to dilution and degradation. Moreover, the facter1 (co-sources L (Living quarters), M (Mining area), A (Agricultural district) and T (tourist area)) contributed 78% of antibiotic concentrations, and the source L was predominant. The results also revealed the prevalence of intL1, sul1 and sul2 in all the sampling sites, and that the abundance of ARGs in the lake was significantly lower (P < 0.01) than that in inflowing rives. Additionally, significant correlations (p < 0.0001) between intL1 and sulfanilamide resistance genes (sul1, sul2) were detected, indicating that intL1 promoted the propagation and they originated from the same anthropogenic sources. Overall, our findings revealed the presence of antibiotics and ARGs and their inconsistent correlations in the Fuxian Lake, which provides a foundation to support further exploration of the occurrence and transmission mechanisms of antibiotics and ARGs.

Broiler Farms and Carcasses Are an Important Reservoir of Multi-Drug Resistant Escherichia coli in Ecuador

Antimicrobial resistance (AMR) is a major health threat for public and animal health in the twenty-first century. In Ecuador, antibiotics have been used by the poultry industry for decades resulting in the presence of multi-drug resistant (MDR) bacteria in the poultry meat production chain, with the consequent risk for public health. This study evaluated the prevalence of ESBL/AmpC and mcr genes in third-generation cephalosporin-resistant Escherichia coli (3GC-R E. coli) isolated from broiler farms (animal component), broiler carcasses (food component), and human enteritis (human component) in Quito-Ecuador. Samples were collected weekly from November 2017 to November 2018. For the animal, food, and human components, 133, 335, and 302 samples were analyzed, respectively. Profiles of antimicrobial resistance were analyzed by an automated microdilution system. Resistance genes were studied by PCR and Sanger sequencing. From all samples, 122 (91.7%), 258 (77%), and 146 (48.3%) samples were positive for 3GC-R E. coli in the animal, food, and human components, respectively. Most of the isolates (472/526, 89.7%) presented MDR phenotypes. The ESBL bla_CTX-M-55, bla_CTX-M-3, bla_CTX-M-15, bla_CTX-M-65, bla_CTX-M-27, and bla_CTX-M-14 were the most prevalent ESBL genes while bla_CMY-2 was the only AmpC detected gene. The mcr-1 gene was found in 20 (16.4%), 26 (10.1%), and 3 (2.1%) of isolates from animal, food, and human components, respectively. The implication of poultry products in the prevalence of ESBL/AmpC and mcr genes in 3GC-R must be considered in the surveillance of antimicrobial resistance.

Use of critically important antimicrobial classes early in life may adversely impact bacterial resistance profiles during adult years: potential co-selection for plasmid-borne fluoroquinolone and macrolide resistance via extended-spectrum beta-lactam use in dairy cattle

The transfer of antimicrobial resistance genes commonly occurs via vertical and horizontal gene transfer, as such genes are often found on the same mobile genetic element. This occurrence can lead to the co-selection of resistance to antimicrobials without their application. Dairy cattle located in the south-western United States were enrolled in a matched-pair longitudinal study to evaluate the effects of a two-dose ceftiofur treatment for metritis on levels of third-generation cephalosporin resistance among faecal Escherichia coli temporally. Escherichia coli chosen for further investigation were isolated on selective media, harboured extended-spectrum beta-lactam, fluoroquinolone and macrolide resistance genes. This combination has previously been unreported; importantly, it included genes encoding for resistance to antibiotics that can only be used in dairy cattle less than 20 months of age. Fluoroquinolones, macrolides and third and higher generation cephalosporins are considered critically important and highest priority for human medicine by the World Health Organization.

Development, spread and persistence of antibiotic resistance genes (ARGs) in the soil microbiomes through co-selection

Bacterial pathogens resistant to multiple antibiotics are emergent threat to the public health which may evolve in the environment due to the co-selection of antibiotic resistance, driven by poly aromatic hydrocarbons (PAHs) and/or heavy metal contaminations. The co-selection of antibiotic resistance (AMR) evolves through the co-resistance or cross-resistance, or co-regulatory mechanisms, present in bacteria. The persistent toxic contaminants impose widespread pressure in both clinical and environmental setting, and may potentially cause the maintenance and spread of antibiotic resistance genes (ARGs). In the past few years, due to exponential increase of AMR, numerous drugs are now no longer effective to treat infectious diseases, especially in cases of bacterial infections. In this mini-review, we have described the role of co-resistance and cross-resistance as main sources for co-selection of ARGs; while other co-regulatory mechanisms are also involved with cross-resistance that regulates multiple ARGs. However, co-factors also support selections, which results in development and evolution of ARGs in absence of antibiotic pressure. Efflux pumps present on the same mobile genetic elements, possibly due to the function of Class 1 integrons (Int1), may increase the presence of ARGs into the environment, which further is promptly changed as per environmental conditions. This review also signifies that mutation plays important role in the expansion of ARGs due to presence of diverse types of anthropogenic pollutants, which results in overexpression of efflux pump with higher bacterial fitness cost; and these situations result in acquisition of resistant genes. The future aspects of co-selection with involvement of systems biology, synthetic biology and gene network approaches have also been discussed.