Erratum: Acquired antibiotic resistance genes: an overview

Antibiotic potentiating effect of Bauhinia purpurea L. against multidrug resistant Staphylococcus aureus

Bauhinia purpurea L. is a medium-sized tree from the family Fabaceae. The plant is traditionally used as medicine by different tribes in Sikkim. The present study aimed to evaluate the modulation in minimum inhibitory concentration (MIC) of the bark methanol extract of Bauhinia purpurea L. against the clinical isolates of multidrug resistant Staphylococcus aureus. The synergistic activity of the test plant extract with different classes of antibiotics was also evaluated. The methanol extract of Bauhinia purpurea exhibited modulation by a 16-fold reduction in the MIC of clindamycin against both resistant and susceptible isolates, followed by penicillin and gentamicin, whereas a maximum of only a 4-fold MIC reduction was observed with ciprofloxacin. The lowest minimum inhibitory concentration and minimum bactericidal concentration showed by the plant extract was 0.48 and 0.97 mg/mL, respectively. The methanol extract of Bauhinia purpurea exhibited synergistic activity with penicillin, gentamicin, ciprofloxacin, and clindamycin against most of the tested isolates of multidrug-resistant Staphylococcus aureus (MDR-SA). Gas chromatography-mass spectrometry analysis of Bauhinia purpurea L. bark methanol extract revealed 16 phytocompounds. The results provide an insight into the potential antibacterial property of the plant extract in terms of its antibiotic MIC modulation and synergistic properties with the selected antibiotics. This is the first report of the antibiotic potentiation property of Bauhinia purpurea L., collected from Sikkim, India.

Effects of Neolamarckia cadamba leaves extract on microbial community and antibiotic resistance genes in cecal contents and feces of broilers challenged with lipopolysaccharides

The effects of Neolamarckia cadamba leaves extract (NCLE), with effective ingredients of flavonoids, on antibiotic resistance genes (ARGs) and relevant microorganisms in cecal contents and feces of broilers treated with or without lipopolysaccharide stimulation (LPS) were investigated. LPS stimulation increased (P < 0.05) the relative abundance of ARGs and mobile genetic elements (MGEs), such as tet(W/N/W), APH(3')-IIIa, ErmB, tet (44), ANT (6)-Ia, tet(O), tet (32), Vang_ACT_CHL, myrA, ANT (6)-Ib, IncQ1, tniB, and rep2 in cecal contents. However, the difference disappeared (P > 0.05) when NCLE was added at the same time. These differential ARGs and MGEs were mainly correlated (P < 0.01) with Clostridiales bacterium, Lachnospiraceae bacterium, and Candidatus Woodwardibium gallinarum. These species increased in LPS-stimulated broilers and decreased when NCLE was applied at the same time. In feces, LPS stimulation decreased (P < 0.05) the relative abundance of tet(Q), adeF, ErmF, Mef(En2), OXA-347, tet (40), npmA, tmrB, CfxA3, and ISCrsp1, while the LPS + NCLE treated group showed no significant effect (P > 0.05) on these ARGs. These differential ARGs and MGEs in feces were mainly correlated (P < 0.01) with Clostridiales bacterium, Pseudoflavonifractor sp. An184, Flavonifractor sp. An10, Ruminococcaceae bacterium, etc. These species increased in LPS-stimulated broilers and increased when NCLE was applied at the same time. In conclusion, LPS stimulation and NCLE influenced microbial communities and associated ARGs in both cecal contents and feces of broilers. NCLE alleviated the change of ARGs and MGEs in LPS-induced broilers by maintaining the microbial balance.IMPORTANCEAntibiotics showed a positive effect on gut health regulation and growth performance improvement in livestock breeding, but the antimicrobial resistance threat and environment pollution problem are increasingly severe with antibiotics abuse. As alternatives, plant extract containing bioactive substances are increasingly used to improve immunity and promote productivity. However, little is known about their effects on diversity and abundance of ARGs. Here, we investigated the effects of NCLE, with effective ingredients of flavonoids, on ARGs and relevant microorganisms in cecal contents and feces of broilers treated with or without lipopolysaccharide stimulation. We found that NCLE reduced the abundance of ARGs in cecal contents of lipopolysaccharide-induced broilers by maintaining the microbial balance. This study provides a comprehensive view of cecal and fecal microbial community, ARGs, and MGEs of broiler following LPS stimulation and NCLE treatment. It might be used to understand and control ARGs dissemination in livestock production.

Antibiotic Resistance in the Finfish Aquaculture Industry: A Review

Significant challenges to worldwide sustainable food production continue to arise from environmental change and consistent population growth. In order to meet increasing demand, fish production industries are encouraged to maintain high growth densities and to rely on antibiotic intervention throughout all stages of development. The inappropriate administering of antibiotics over time introduces selective pressure, allowing the survival of resistant bacterial strains through adaptive pathways involving transferable nucleotide sequences (i.e., plasmids). This is one of the essential mechanisms of antibiotic resistance development in food production systems. This review article focuses on the main international regulations and governing the administering of antibiotics in finfish husbandry and summarizes recent data regarding the distribution of bacterial resistance in the finfish aquaculture food production chain. The second part of this review examines promising alternative approaches to finfish production, sustainable farming techniques, and vaccination that circumvents excessive antibiotic use, including new animal welfare measures. Then, we reflect on recent adaptations to increasingly interdisciplinary perspectives in the field and their greater alignment with the One Health initiative.

Fate of Antibiotic Resistance Genes and Changes in Bacterial Community With Increasing Breeding Scale of Layer Manure

The use of antimicrobials in intensive poultry production is becoming increasingly common because of its high throughput of meat and egg products. However, the profile of antibiotic resistance genes (ARGs) and the underlying mechanisms in different breeding scale farms were not fully explored. The study examined the profiles of ARGs in layer manure from three free-range and 12 intensive layer farms with different scales (N500, N5000, N10000, and N20000). A quantitative PCR (qPCR) array was used to quantify ARGs, and microbial community structure was analyzed by 16S rRNA gene sequencing. A total of 48 ARGs, belonging to seven major types, were identified in the layer manure samples, with sul2, tetM-01, and ermB being the predominant ones. The abundance, diversity, and mobility potential of ARGs in layer manure changed significantly with the increasing of the breeding scale. The abundances of total ARGs had significantly positive correlations with mobile genetic elements (MGEs), suggesting the mobility potential of ARGs in layer manure samples. Bacterial abundance did not show significant differences among the five group manure samples. However, bacterial diversity showed an increasing trend along the breeding scale. Pathogenic Bacteroidetes increased in the largest-scale layer manure samples and showed significant positive correlations with most ARGs. Network analysis revealed significant co-occurrence patterns between ARGs and microbial taxa, indicating ARGs had a wide range of bacterial hosts. Proteobacteria and Firmicutes were potential hosts for tetracycline and macrolide-lincosamide-streptogramin B (MLSB) resistant genes. Our results indicated that the expansion of the breeding scale of a farm promotes the abundance, diversity, and mobility potential of ARGs in layer manure.

Antimicrobial Resistance of E. coli and Salmonella Isolated from Wild Birds in a Rehabilitation Center in Turkey

Wildlife plays a critical role as a reservoir for zoonosis especially pathogenic enteric bacteria. In this study we evaluated the presence of E. coli and Salmonella isolates from wild birds and determined their antimicrobial resistance. Intestine and fecal samples from 82 dead wild birds obtained from rehabilitation centre, were examined by microbiological analysis, antibiotic susceptibilities against of 18 antimicrobials and presence of tetracycline resistance genes by multiplex and singleplex PCR were investigated. A total of 51 E. coli were identified as well as Salmonella Kentucky and Salmonella Bisberg. A majority of the E. coli isolates were resistant to lincomysin (100%), penicilline (96.1%), kanamycin (80.4%), tetracycline (68.6%), and oxytetracycline (64.7%). All Salmonella serotypes were resistant to lincomycin, nalidixic acid and penicilline.In addition, 58.82% of E. coli isolates had phenotypic resistance to at least three or more antimicrobials. Our results indicated that the high frequency of tetracycline resistance (68.62%) due to the tet (A), tet (B), and tet (D) genes. This is the first report isolating S. Bisberg and determining antibiotic susceptibility of E.coli and Salmonella isolates from wild birds in Turkey. These results will help providing better understand of the dissemination of antibiotic resistancy in the environment, which can be used to potentially decrease spread through bird migration. Moreover, these results help assess the risk of spread of resistance from wild birds to humans.

Contamination of antibiotics and sul and tet(M) genes in veterinary wastewater, river, and coastal sea in Thailand

Water systems in Southeast Asia accumulate antibiotics and antibiotic resistance genes (ARGs) from multiple origins, notably including human clinics and animal farms. To ascertain the fate of antibiotics and ARGs in natural water environments, we monitored the concentrations of these items in Thailand. Here, we show high concentrations of tetracyclines (72,156.9 ng/L) and lincomycin (23,968.0 ng/L) in pig farms, followed by nalidixic acid in city canals. The city canals and rivers contained diverse distributions of antibiotics and ARGs. Assessments of targeted ARGs, including sul1, sul2, sul3, and tet(M), showed that freshwater (pig farm wastewater, rivers, and canals) consistently contained these ARGs, but these genes were less abundant in seawater. Although sulfonamides were low concentrations (<170 ng/mL), sul1 and sul2 genes were abundant in freshwater (minimum 4.4 × 10^-3-maximum 1.0 × 10⁰ copies/16S), suggesting that sul genes have disseminated over a long period, despite cessation of use of this class of antibiotics. Ubiquitous distribution of sul genes in freshwater appeared to be independent of selection pressure. In contrast, water of the coastal sea in the monitored area was not contaminated by these antibiotics or ARGs. The density of Enterobacteriales was lower in seawater than in freshwater, suggesting that the number of ARG-possessing Enterobacteriales falls after entering seawater. From the pig farms, through rivers/canals, to the coastal sea, the occurrence of tetracyclines and tet(M) exhibited some correlation, although not a strong one. However, no correlations were found between concentrations of total antibiotics and ARGs, nor between sulfonamides and sul genes. This is the first comprehensive study showing Thai features of antibiotics and ARGs contaminations. The pig farm is hot spot of antibiotics and ARGs, and sul genes ubiquitously distribute in freshwater environments, which become less abundant in seawater.

Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida

Macrolides have been effective clinical antibiotics for over 70 years. They inhibit protein biosynthesis in bacterial pathogens by narrowing the nascent protein exit tunnel in the ribosome. The macrolide class of natural products consist of a macrolactone ring linked to one or more sugar molecules. Most of the macrolides used currently are semi-synthetic erythromycin derivatives, composed of a 14- or 15-membered macrolactone ring. Rapidly emerging resistance in bacterial pathogens is among the most urgent global health challenges, which render many antibiotics ineffective, including next-generation macrolides. To address this threat and advance a longer-term plan for developing new antibiotics, we demonstrate how 16-membered macrolides overcome erythromycin resistance in clinically isolated Staphylococcus aureus strains. By determining the structures of complexes of the large ribosomal subunit of Deinococcus radiodurans (D50S) with these 16-membered selected macrolides, and performing anti-microbial studies, we identified resistance mechanisms they may overcome. This new information provides important insights toward the rational design of therapeutics that are effective against drug resistant human pathogens.

Rapid antibiotic susceptibility testing using resazurin bulk modified screen-printed electrochemical sensing platforms

Urinary tract infections (UTIs) are one of the most common types of bacterial infection. UTIs can be associated with multidrug resistant bacteria and current methods of determining an effective antibiotic for UTIs can take up to 48 hours, which increases the chances of a negative prognosis for the patient. In this paper we report for the first time, the fabrication of resazurin bulk modified screen-printed macroelectrodes (R-SPEs) demonstrating them to be effective platforms for the electrochemical detection of antibiotic susceptibility in complicated UTIs. Using differential pulse voltammetry (DPV), resazurin was able to be detected down to 15.6 μM. R-SPEs were utilised to conduct antibiotic susceptibility testing (AST) of E. coli (ATCC® 25922) to the antibiotic gentamicin sulphate using DPV to detect the relative concentrations of resazurin between antibiotic treated bacteria, and bacteria without antibiotic treatment. Using R-SPEs, antibiotic susceptibility was determined after a total elapsed time of 90 minutes including the inoculation of the artificial urine, preincubation and testing time. The use of electrochemistry as a phenotypic means of identifying an effective antibiotic to treat a complicated UTI offers a rapid and accurate alternative to culture based methods for AST with R-SPEs offering an inexpensive and simpler alternative to other AST methods utilising electrochemical based approaches.

First Survey on the Presence and Distribution of Oxytetracycline-Resistance Genes in Anaplasma Species

INTRODUCTION

Anaplasma sp. is an obligatory intracellular Gram-negative tick-transmitted bacterial pathogen of humans and animals. Oxytetracycline and chlortetracycline are the drugs of choice for treating domestic animals with acute anaplasmosis. Lack of documented information about oxytetracycline resistance in Anaplasma species in the world was the scope of this study to screen by PCR for the detection of the oxytetracycline-resistance genes in Anaplasma species from infected cattle and sheep in the Northwest and Southwest of Iran.

MATERIALS AND METHODS

Total of 100 cattle and sheep blood samples collected from 2 provinces in the Northwest and 1 province in the Southwest of Iran were tested microscopically by the Giemsa staining examination and confirmed by PCR. Then the presence of two different oxytetracycline-resistance genes (otrA, and otrB) was detected by PCR in positive samples.

RESULTS

The results showed that 60% of Anaplasma-infected samples were identified to have an otrA-resistance gene, and 26.67% had an otrB-resistance gene. The coexistence of two oxytetracycline-resistance determinants was encountered in 13.33% of the isolates. The significant difference in the frequency of otr genes was found among three Anaplasma species (A. marginale, A. centrale and A. ovis), and among three studied regions in Iran (p < 0.05). The identified sequences were submitted to the GenBank and deposited under accession numbers MN880729 and MN895439 for otrB and otrA genes.

CONCLUSION

This study, for the first time, indicated the oxytetracycline-resistance genes in the three most prevalent Anaplasma species in ruminants. This finding helps to select an appropriate treatment strategy for eradication of anaplasmosis.

Faecal microbiota and antimicrobial resistance gene profiles of healthy foals

BACKGROUND

The human and domestic animal faecal microbiota can carry various antimicrobial resistance genes (ARGs), especially if they have been exposed to antimicrobials. However, little is known about the ARG profile of the faecal microbiota of healthy foals. A high-throughput qPCR array was used to detect ARGs in the faecal microbiota of healthy foals.

OBJECTIVES

To characterise the faecal microbiota and ARG profiles in healthy Australian foals aged less than 1 month.

STUDY DESIGN

Observational study.

METHODS

The faecal microbiota and ARG profiles of 37 Thoroughbred foals with no known gastrointestinal disease or antimicrobial treatment were determined using 16S rRNA gene sequencing and a high-throughput ARG qPCR array. Each foal was sampled on one occasion.

RESULTS

Firmicutes and Bacteroidetes were dominant in the faecal microbiota. Foals aged 1-2 weeks had significantly lower microbiota richness than older foals. Tetracycline resistance genes were the most common ARGs in the majority of foals, regardless of age. ARGs of high clinical concern were rarely detected in the faeces. The presence of ARGs was associated with the presence of class I integron genes.

MAIN LIMITATIONS

Samples were collected for a case-control study so foals were not sampled longitudinally, and thus the development of the microbiota as individual foals aged could not be proven. The history of antimicrobial treatment of the dams was not collected and may have affected the microbiota of the foals.

CONCLUSION

The ARGs in foal faeces varied concomitantly with age-related microbiota shifts. The high abundance of tetracycline resistance genes was likely due to the dominance of Bacteroides spp.

Synergistic effects of anti-MRSA herbal extracts combined with antibiotics

MRSA is a super drug-resistant bacterium. Developing new drug or therapeutic strategies against MRSA is urgently needed. Increasing evidence has shown that herbal extracts and antibiotics can have synergistic effects against MRSA. This review focuses on commonly used antibiotics combined with herbal extracts against MRSA and the corresponding mechanisms. Through systematic analysis, we found that herbal extracts combined with antibiotics, such as β-lactams, quinolones, aminoglycosides, tetracyclines and glycopeptides, could greatly enhance the antibacterial effects of the antibiotics, reduce the dosage and toxic side effects, and reverse MRSA resistance. Therefore, we conclude that herbal extracts combined with antibiotics may be a promising strategy to combat MRSA. This review provides a novel idea for overcoming antibiotic resistance.

Tetracycline Resistance Gene Profiles in Red Seabream (Pagrus major) Intestine and Rearing Water After Oxytetracycline Administration

Marine aquaculture fish and the environment are possible hot spots for the maintenance and spread of antibiotic resistance genes (ARGs). We here show the time courses of changes of six tetracycline resistance genes (tet) in fish rearing seawater and fish intestine in tank experiments. Experimental tanks were prepared as oxytetracycline (OTC) administration tanks and those without OTC. It was found that tet(B), tet(M), and tet(W) were dominant in seawater among the six tet genes. tet(B) and tet(M) abundances increased immediately after OTC administration, indicating that OTC served as a selective pressure to increase the proportion of tet-possessing bacteria. In contrast, the abundance of tet genes in the fish intestine did not differ between the with- and without-OTC administration groups, and clearly was not altered by OTC administration. Profile changing of tet in seawater and fish intestine did not synchronize. These observations suggested that the dynamics of intestinal tet-possessing bacteria do not directly reflect the environment, but reflect selection within the intestine.

Tracking Antimicrobial Resistance Determinants in Diarrheal Pathogens: A Cross-Institutional Pilot Study

Infectious diarrhea affects over four billion individuals annually and causes over a million deaths each year. Though not typically prescribed for treatment of uncomplicated diarrheal disease, antimicrobials serve as a critical part of the armamentarium used to treat severe or persistent cases. Due to widespread over- and misuse of antimicrobials, there has been an alarming increase in global resistance, for which a standardized methodology for geographic surveillance would be highly beneficial. To demonstrate that a standardized methodology could be used to provide molecular surveillance of antimicrobial resistance (AMR) genes, we initiated a pilot study to test 130 diarrheal pathogens (Campylobacter spp., Escherichia coli, Salmonella, and Shigella spp.) from the USA, Peru, Egypt, Cambodia, and Kenya for the presence/absence of over 200 AMR determinants. We detected a total of 55 different determinants conferring resistance to ten different categories of antimicrobials: genes detected in ≥ 25 samples included bla_TEM, tet(A), tet(B), mac(A), mac(B), aadA1/A2, strA, strB, sul1, sul2, qacEΔ1, cmr, and dfrA1. The number of determinants per strain ranged from none (several Campylobacter spp. strains) to sixteen, with isolates from Egypt harboring a wider variety and greater number of genes per isolate than other sites. Two samples harbored carbapenemase genes, bla_OXA-48 or bla_NDM. Genes conferring resistance to azithromycin (ere(A), mph(A)/mph(K), erm(B)), a first-line therapeutic for severe diarrhea, were detected in over 10% of all Enterobacteriaceae tested: these included >25% of the Enterobacteriaceae from Egypt and Kenya. Forty-six percent of the Egyptian Enterobacteriaceae harbored genes encoding CTX-M-1 or CTX-M-9 families of extended-spectrum β-lactamases. Overall, the data provide cross-comparable resistome information to establish regional trends in support of international surveillance activities and potentially guide geospatially informed medical care.

The use of aminoglycosides in animals within the EU: development of resistance in animals and possible impact on human and animal health: a review

Aminoglycosides (AGs) are important antibacterial agents for the treatment of various infections in humans and animals. Following extensive use of AGs in humans, food-producing animals and companion animals, acquired resistance among human and animal pathogens and commensal bacteria has emerged. Acquired resistance occurs through several mechanisms, but enzymatic inactivation of AGs is the most common one. Resistance genes are often located on mobile genetic elements, facilitating their spread between different bacterial species and between animals and humans. AG resistance has been found in many different bacterial species, including those with zoonotic potential such as Salmonella spp., Campylobacter spp. and livestock-associated MRSA. The highest risk is anticipated from transfer of resistant enterococci or coliforms (Escherichia coli) since infections with these pathogens in humans would potentially be treated with AGs. There is evidence that the use of AGs in human and veterinary medicine is associated with the increased prevalence of resistance. The same resistance genes have been found in isolates from humans and animals. Evaluation of risk factors indicates that the probability of transmission of AG resistance from animals to humans through transfer of zoonotic or commensal foodborne bacteria and/or their mobile genetic elements can be regarded as high, although there are no quantitative data on the actual contribution of animals to AG resistance in human pathogens. Responsible use of AGs is of great importance in order to safeguard their clinical efficacy for human and veterinary medicine.

Antibiotic Resistance Genes in Antibiotic-Free Chicken Farms

Rising concern about the use of antibiotics in food production has resulted in many studies on the occurrence of antibiotic resistance genes (ARGs) in animal-associated bacterial communities. There are few baseline data on the abundance of ARGs on farms where chickens are intensively raised with little or no use of antibiotics. This study used a high-throughput quantitative PCR array to survey two antibiotic-free chicken farms for the occurrence of ARGs and mobile genetic elements known to enhance the spread of ARGs. No antibiotics had been used on the study farms for five years prior to this study. The results provide a baseline for the occurrence of resistance genes in the chicken production system without direct selective pressure.

Detection of fecal bacteria and antibiotic resistance genes in drinking water collected from three First Nations communities in Manitoba, Canada

This study analyzed the microbiological quality of drinking and source water from three First Nations communities in Manitoba, Canada that vary with respect to the source, storage and distribution of drinking water. Community A relies on an aquifer and Community B on a lake as source water to their water treatment plants. Community C does not have a water treatment plant and uses well water. Quantification of free residual chlorine and fecal bacterial (E. coli and coliforms), as well as detection of antibiotic resistance genes (sul, ampC, tet(A), mecA, vanA, blaSHV, blaTEM, blaCTX-M, blaOXA-1, blaCYM-2, blaKPC, blaOXA-48, blaNDM, blaVIM, blaGES and blaIMP) was carried out. While water treatment plants were found to be working properly, as post-treatment water did not contain E. coli or coliforms, once water entered the distribution system, a decline in the chlorine concentration with a concomitant increase in bacterial counts was observed. In particular, water samples from cisterns not only contained high number of E. coli and coliforms, but were also found to contain antibiotic resistance genes. This work shows that proper maintenance of the distribution and storage systems in First Nations communities is essential in order to provide access to clean and safe drinking water.

[Results of the observational (non-interventional) research 'Analysis of therapeutic efficiency of the polyvalent Piobacteriophag (Secstaphag) in the treatment of acute sinusitis']

He article describes an observational (non-intervening) research 'Analysis of the therapeutic efficacy of the Polyvalent Piobacteriophage (secstafag) in the treatment of acute sinusitis'. The obtained results prove the effectiveness of the drug in the treatment of this ENT pathology.

Freshwater salmon aquaculture in Chile and transferable antimicrobial resistance

Large amounts of antimicrobials are used in salmonid aquaculture in Chile. Most are used in marine aquaculture, but appreciable amounts are also employed in freshwater aquaculture. Much research and many publications have examined transferable antimicrobial resistance in bacteria isolated from marine salmon farms, but much less attention has been paid to this area in freshwater salmon farming. A recent paper by Domínguez et al. (2019) has as least in part remedied this situation. We now comment on some of its interpretations and have attempted to point out its areas of strength and weakness in light of the published scientific literature. Seen in this setting, the important results presented by Domínguez et al. (2019) underline the need for increased awareness of the challenge to animal and human health posed by excessive use of antimicrobials in aquaculture.

Effect of tetracycline treatment regimens on antibiotic resistance gene selection over time in nursery pigs

Background

The majority of antimicrobials given during the production of pigs are given to nursery pigs. The influence of antimicrobial use on the levels of antimicrobial resistant (AMR) genes is important to quantify to be able to assess the impact of resistance on the food chain and risk to human and animal health.

Results

This study investigated the response on the levels of nine AMR genes to five different treatment strategies with oxytetracycline, and the dynamics of gene abundance over time by following 1167 pigs from five different farms in Denmark.

The results showed no significant difference between treatments and an increase in abundance for the efflux pump encoding tet(A) gene and the genes encoding the ribosomal protection proteins tet(O) and tet(W) tetracycline resistant genes following treatment, while tet(M) showed no response to treatment. However, it was also observed that the levels of tet(O), tet(W), and ermB in some farms would drift more over time compared to a single treatment-course with antibiotic.

Conclusion

This study underlines the large variation in AMR levels under natural conditions and the need for increased investigation of the complex interactions of antimicrobial treatment and other environmental and managerial practices in swine production on AMR gene abundance.

Comparative Analysis of Pasteurella multocida Isolates from Acute and Chronic Fowl Cholera Cases in Hungary During the Period 2005 Through 2010

Fowl cholera (FC) is a highly contagious and economically important disease of poultry worldwide. This study was performed on 218 Pasteurella multocida isolates collected from separated breeding farms or backyards with acute and chronic FC cases in multiple localities across Hungary during the period 2005-2010. All isolates were characterized by a broad range of biochemical, serological, and molecular methods, as well as their antibiotic susceptibility to aminoglycosides (A), macrolides (M), penicillins (P), quinolones (Q), cephalosporins, sulphonamides (S), and tetracyclines (T) was determined. Fifty-two percent of all isolates belonged to a well-defined type that was highly virulent, caused acute FC, and had the same character: fermented L-arabinose, possessed capsule type A, identified as Heddleston serotype 1, and possessed allele type A of the ptfA fimbrial gene. This type was widely distributed among poultry in Hungary, especially in waterfowl flocks. Isolates collected from the chronic FC cases were more diverse: none of them fermented L-arabinose; they possessed capsule type A (76%), F (9%), or was non-typeable (15%) with different Heddleston serotypes, mainly 1, 3, 4, and 5, or 7 and 16; in addition, possessed allele type B of ptfA fimbrial gene. Only 26 isolates presented characters similar to any of the chronic FC cases but caused severe disease. The antibiotic susceptibility assay presented that 80% of all isolates were resistant to 1-5 of the studied antimicrobial agents. During the survey, after two years, there was a dramatic decline both in the number of the multi-drug resistance phenotypes and the prevalence of the highly virulent type of the isolates. In the next four years, multiresistant isolates were almost completely removed, whereas the number of isolates resistant to 1 or 2 drugs was constant. Reduced frequency of antibiotic multiresistant, mostly L-arabinose-fermenting isolates, has been observed since 2007. This reduction may be a consequence of the elimination of multiple waterfowl flocks in Hungary during avian influenza outbreaks, which possibly created a break in the "transmission chain" of pathogenic P. multocida isolates.

Occurrence of sul and tet(M) genes in bacterial community in Japanese marine aquaculture environment throughout the year: Profile comparison with Taiwanese and Finnish aquaculture waters

The use of antibiotics in aquaculture causes selection pressure for antibiotic-resistant bacteria (ARB). Antibiotic resistance genes (ARGs) may persist in ARB and the environment for long time even after stopping drug administration. Here we show monthly differences in the occurrences of genes conferring resistance to sulfonamides (i.e. sul1, sul2, sul3), and tetracyclines (tet(M)) in Japanese aquaculture seawater accompanied by records of drug administration. sul2 was found to persist throughout the year, whereas the occurrences of sul1, sul3, and tet(M) changed month-to-month. sul3 and tet(M) were detected in natural bacterial assemblages in May and July, but not in colony-forming bacteria, thus suggesting that the sul3 was harbored by the non-culturable fraction of the bacterial community. Comparison of results from Taiwanese, Japanese, and Finnish aquaculture waters reveals that the profile of sul genes and tet(M) in Taiwan resembles that in Japan, but is distinct from that in Finland. To our knowledge, this work represents the first report to use the same method to compare the dynamics of sul genes and tet(M) in aquaculture seawater in different countries.

A Novel Trimethoprim Resistance Gene, dfrA36, Characterized from Escherichia coli from Calves

The presence of dfrA35 associated with ISCR2 in Escherichia coli from animals, as well as its presence in other E. coli strains from different sources and countries and in Acinetobacter, highlights the global spread of this gene and its potential for further dissemination. The genetic link of ISCR2-dfrA35 with other antibiotic and disinfectant resistance genes showed that multidrug-resistant E. coli may be selected and maintained by the use of either one of several antimicrobials.

Whole-genome sequencing of trimethoprim-resistant Escherichia coli strains MF2165 and PF9285 from healthy Swiss fattening calves revealed a so far uncharacterized dihydrofolate reductase gene, dfrA35. Functionality and association with trimethoprim resistance were demonstrated by cloning and expressing dfrA35 in E. coli. The DfrA35 protein showed the closest amino acid identity (49.4%) to DfrA20 from Pasteurella multocida and to the Dfr determinants DfrG (41.2%), DfrD (40.8%), and DfrK (40.0%) found in Gram-positive bacteria. The dfrA35 gene was integrated within a florfenicol/chloramphenicol-sulfonamide resistance ISCR2 element (floR-ISCR2-dfrA35-sul2) next to a Tn21-like transposon that contained genes with resistance to sulfonamides (sul1), streptomycin (aadA1), gentamicin/tobramycin/kanamycin (aadB), and quaternary ammonium compounds (qacEΔ1). A search of GenBank databases revealed that dfrA35 was present in 26 other E. coli strains from different origins as well as in Acinetobacter.

IMPORTANCE The presence of dfrA35 associated with ISCR2 in Escherichia coli from animals, as well as its presence in other E. coli strains from different sources and countries and in Acinetobacter, highlights the global spread of this gene and its potential for further dissemination. The genetic link of ISCR2-dfrA35 with other antibiotic and disinfectant resistance genes showed that multidrug-resistant E. coli may be selected and maintained by the use of either one of several antimicrobials.

Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 Escherichia coli Strain Sanji with Novel In Silico Serotype O89b:H9

E. coli strain Sanji is the first sequenced and analyzed genome of the recently emerged pathogenic XDR strains with sequence type ST167 and novel in silico serotype O89b:H9. Comparison of the genomes of Sanji with other ST167 strains revealed distinct sets of different plasmids, mobile IS elements, and antibiotic resistance genes in each genome, indicating that there exist multiple paths toward achieving XDR. The emergence of these pathogenic ST167 E. coli strains with diverse XDR capabilities highlights the difficulty of preventing or mitigating the development of XDR properties in bacteria and points to the importance of better understanding of the shared underlying virulence mechanisms and physiology of pathogenic bacteria.

Extensive drug resistance (XDR) is an escalating global problem. Escherichia coli strain Sanji was isolated from an outbreak of pheasant colibacillosis in Fujian province, China, in 2011. This strain has XDR properties, exhibiting sensitivity to carbapenems but no other classes of known antibiotics. Whole-genome sequencing revealed a total of 32 known antibiotic resistance genes, many associated with insertion sequence 26 (IS26) elements. These were found on the Sanji chromosome and 2 of its 6 plasmids, pSJ_255 and pSJ_82. The Sanji chromosome also harbors a type 2 secretion system (T2SS), a type 3 secretion system (T3SS), a type 6 secretion system (T6SS), and several putative prophages. Sanji and other ST167 strains have a previously uncharacterized O-antigen (O89b) that is most closely related to serotype O89 as determined on the basis of analysis of the wzm-wzt genes and in silico serotyping. This O89b-antigen gene cluster was also found in the genomes of a few other pathogenic sequence type 617 (ST617) and ST10 complex strains. A time-scaled phylogeny inferred from comparative single nucleotide variant analysis indicated that development of these O89b-containing lineages emerged about 30 years ago. Comparative sequence analysis revealed that the core genome of Sanji is nearly identical to that of several recently sequenced strains of pathogenic XDR E. coli belonging to the ST167 group. Comparison of the mobile elements among the different ST167 genomes revealed that each genome carries a distinct set of multidrug resistance genes on different types of plasmids, indicating that there are multiple paths toward the emergence of XDR in E. coli.

IMPORTANCEE. coli strain Sanji is the first sequenced and analyzed genome of the recently emerged pathogenic XDR strains with sequence type ST167 and novel in silico serotype O89b:H9. Comparison of the genomes of Sanji with other ST167 strains revealed distinct sets of different plasmids, mobile IS elements, and antibiotic resistance genes in each genome, indicating that there exist multiple paths toward achieving XDR. The emergence of these pathogenic ST167 E. coli strains with diverse XDR capabilities highlights the difficulty of preventing or mitigating the development of XDR properties in bacteria and points to the importance of better understanding of the shared underlying virulence mechanisms and physiology of pathogenic bacteria.

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Mechanisms of Bacterial Resistance to Antimicrobial Agents

During the past decades resistance to virtually all antimicrobial agents has been observed in bacteria of animal origin. This chapter describes in detail the mechanisms so far encountered for the various classes of antimicrobial agents. The main mechanisms include enzymatic inactivation by either disintegration or chemical modification of antimicrobial agents, reduced intracellular accumulation by either decreased influx or increased efflux of antimicrobial agents, and modifications at the cellular target sites (i.e., mutational changes, chemical modification, protection, or even replacement of the target sites). Often several mechanisms interact to enhance bacterial resistance to antimicrobial agents. This is a completely revised version of the corresponding chapter in the book Antimicrobial Resistance in Bacteria of Animal Origin published in 2006. New sections have been added for oxazolidinones, polypeptides, mupirocin, ansamycins, fosfomycin, fusidic acid, and streptomycins, and the chapters for the remaining classes of antimicrobial agents have been completely updated to cover the advances in knowledge gained since 2006.

Aminoglycoside-modifying enzyme and 16S ribosomal RNA methyltransferase genes among a global collection of Gram-negative isolates

OBJECTIVES

The prevalence of genes encoding aminoglycoside-modifying enzymes (AMEs) and 16S rRNA methyltransferases among 200 Gram-negative clinical isolates resistant to different aminoglycosides and collected worldwide during 2013 was evaluated.

METHODS

Selected AMEs and 16S rRNA methyltransferase genes were screened by PCR/sequencing among 49 Acinetobacter spp., 52 Pseudomonas aeruginosa and 99 Enterobacterales.

RESULTS

In total 72 isolates carried aac(6')-lb variants (36.0% overall; 55.6% Enterobacterales): 30 aac(6')-Ib-cr, 21 aac(6')-Ib and 21 aac(6')-Ib-like displaying substitutions L119S (alone or in combination with V71A or R173K) or S100G. Ten aph(3')-VI variants were detected among 35 isolates (46.9% of Acinetobacter spp.). Nineteen isolates carried variants of aac(3)-I, with aac(3)-Ia (n=13, mostly Acinetobacter spp.) being the most prevalent. Other AME genes detected were ant(3″)-Ia (n=41), ant(2″)-Ia (n=24), aac(3)-IIe (n=23), aac(3)-IId (n=21), aac(6')-Im (n=13, mostly P. aeruginosa), aacA8 (n=3), aac(3)-IIf (n=1) and aac(3)-IVa (n=1). Among 42 isolates resistant to amikacin, gentamicin and tobramycin tested for 16S rRNA methyltransferase genes, 21 (50.0%) tested positive; armA was most common (n=14), but 4 isolates carried rmtB1, 2 rmtF1 and 1 new variant rmtB4. Over 60 gene combinations, consisting of one to four AMEs and 16S rRNA methyltransferases, were observed. Cloning genes not previously characterised revealed diverse aminoglycoside resistance patterns for some AMEs, but expected results for rmtB4.

CONCLUSIONS

Studies broadly evaluating these aminoglycoside resistance genes are needed. Using agents stable in the presence of these resistance genes might help overcome resistance.

Rapid pathogen identification using a novel microarray-based assay with purulent meningitis in cerebrospinal fluid

In order to improve the diagnosis of pathogenic bacteria in cerebrospinal fluid (CSF) with purulent meningitis, we developed a DNA microarray technique for simultaneous detection and identification of seven target bacterium. DNA were extracted from 24 CSF samples with purulent meningitis (or suspected purulent meningitis). The specific genes of each pathogen were chosen as the amplification target, performed the polymerase chain reaction (PCR), labeled with a fluorescence dye, and hybridized to the oligonucleotide probes on the microarray. There is no significant cross-hybridization fluorescent signal occurred in untargeted bacteria. There were 87.5% (21/24) positive results in DNA microarray compared with the 58.3% (14/24) of the CSF culture test. Of which 58.3% (14/24) of the patients with culture-confirmed purulent meningitis, 37.5% (9/24) patients who were not confirmed by culture test but were demonstrated by the clinical diagnosis and DNA microarray. Multiple bacterial infections were detected in 5 cases by the microarray. In addition, the number of gene copies was carried out to determine the sensitivity of this technique, which was shown to be 3.5 × 10¹ copies/μL. The results revealed that the microarray technique which target pathogens of the CSF specimen is better specificity, accuracy, and sensitivity than traditional culture method. The microarray method is an effective tool for rapidly detecting more target pathogens and identifying the subtypes of strains which can eliminate the impact of the different individuals with purulent meningitis for prompt diagnosis and treatment.

Tetracycline resistance gene tet(M) of a marine bacterial strain is not accumulated in bivalves from seawater in clam tank experiment and mussel monitoring

Antibiotic resistance genes (ARGs) are found in marine as well as terrestrial bacteria. Bivalves are known to accumulate chemical pollutants and pathogenic microbes, however, the fate of ARGs in bivalves after the intake of ARG-possessing bacteria is not known. Here we show that the copy number of oxytetracycline resistance gene tet(M) increased rapidly in the clam digestive tract by filtering water, then remained constant over 96h in a tank experiment even with the addition of tet(M)-possessing bacteria every 24h. >99.9% of the added tet(M) was decomposed, reaching a balanced state. Environmental sampling of mussel digestive tract and seawater supported the hypothesis that tet(M) was decomposed in bivalves as tet(M) was present in seawater from April to October at a concentration of 10^-5 to 10^-6 copies/16S, whereas tet(M) in mussels was mostly below the detection limit. Two (April) and three (July and October) individual mussels were positive for tet(M) with a concentration equivalent to that of seawater. We therefore conclude that bivalves do not accumulate tet(M) from seawater.

Antimicrobial Resistance among Staphylococci of Animal Origin

Antimicrobial resistance among staphylococci of animal origin is based on a wide variety of resistance genes. These genes mediate resistance to many classes of antimicrobial agents approved for use in animals, such as penicillins, cephalosporins, tetracyclines, macrolides, lincosamides, phenicols, aminoglycosides, aminocyclitols, pleuromutilins, and diaminopyrimidines. In addition, numerous mutations have been identified that confer resistance to specific antimicrobial agents, such as ansamycins and fluoroquinolones. The gene products of some of these resistance genes confer resistance to only specific members of a class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents, including agents approved solely for human use. The resistance genes code for all three major resistance mechanisms: enzymatic inactivation, active efflux, and protection/modification/replacement of the cellular target sites of the antimicrobial agents. Mobile genetic elements, in particular plasmids and transposons, play a major role as carriers of antimicrobial resistance genes in animal staphylococci. They facilitate not only the exchange of resistance genes among members of the same and/or different staphylococcal species, but also between staphylococci and other Gram-positive bacteria. The observation that plasmids of staphylococci often harbor more than one resistance gene points toward coselection and persistence of resistance genes even without direct selective pressure by a specific antimicrobial agent. This chapter provides an overview of the resistance genes and resistance-mediating mutations known to occur in staphylococci of animal origin.

Characterization and mechanism analysis of lincomycin biodegradation with Clostridium sp. strain LCM-B isolated from lincomycin mycelial residue (LMR)

Lincomycin mycelial residue (LMR) is the restricted resource because it contains residual lincomycin, which is producing potential risks to the environment and human health. In this study, lincomycin-degrading strain LCM-B was isolated and identified as Clostridium sp. in the LMR. Strain LCM-B was able to degrade 62.03% of lincomycin at the initial concentration of 100 mg L^-1 after incubation for 10 d, while only 15.61% of lincomycin was removed at the initial concentration of 500 mg L^-1. The removal efficiency of lincomycin by strain LCM-B decreased as the initial concentration increased. Gene lnuB (which encodes the nucleotidyl transferase) was detected in the isolated strain, and it was proven to participate in lincomycin biodegradation based on the analysis of degradation products and pathway. The results provide a relatively complete understanding of lincomycin biodegradation mechanism. Strain LCM-B is promising to eliminate lincomycin from the LMR.

IncA/C plasmids conferring high azithromycin resistance in vibrio cholerae

Azithromycin (AZM) is a clinically important antibiotic against Vibrio cholerae, especially for inhibiting V. cholerae colonisation of the intestine and for the treatment of severe cholera in children and pregnant women. An IncA/C plasmid was isolated from two high minimum inhibitory concentration (MIC) AZM-resistant V. cholerae strains of the two mainly pathogenic serogroups (O1 and O139) isolated in China. In the 172 predicted open reading frames (ORFs), 16 genes were related to antibiotic resistance, of which 5 were well-defined genes associated with macrolide resistance. The five macrolide resistance genes distributed in two clusters, mphR-mrx-mph(K) and mel-mph2, flanked by insertion sequence elements and involving two kinds of resistance mechanism. Deletion of the complete region of the two clusters deceased the AZM MIC from ≥64 µg/mL to ≤0.5 µg/mL. This IncA/C plasmid shows great ability to accumulate antibiotic resistance genes. In addition to 11 resistance genes to other antibiotics, 5 macrolide resistance genes with different function were gathered repeatedly through transposition on one plasmid. This genotype could not be simply explained by antibiotic stress applied on the host from the environment or treatment. These phosphorylases and transmembrane transporters might be involved in the transport and metabolism of other non-antibiotic substances, enabling this kind of plasmid to propagate better in the host.

Bacteria from Animals as a Pool of Antimicrobial Resistance Genes

Antimicrobial agents are used in both veterinary and human medicine. The intensive use of antimicrobials in animals may promote the fixation of antimicrobial resistance genes in bacteria, which may be zoonotic or capable to transfer these genes to human-adapted pathogens or to human gut microbiota via direct contact, food or the environment. This review summarizes the current knowledge of the use of antimicrobial agents in animal health and explores the role of bacteria from animals as a pool of antimicrobial resistance genes for human bacteria. This review focused in relevant examples within the ESC(K)APE (Enterococcus faecium, Staphylococcus aureus, Clostridium difficile (Klebsiella pneumoniae), Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae) group of bacterial pathogens that are the leading cause of nosocomial infections throughout the world.

Type B Chloramphenicol Acetyltransferases Are Responsible for Chloramphenicol Resistance in Riemerella anatipestifer, China

Riemerella anatipestifer causes serositis and septicaemia in domestic ducks, geese, and turkeys. Traditionally, the antibiotics were used to treat this disease. Currently, our understanding of R. anatipestifer susceptibility to chloramphenicol and the underlying resistance mechanism is limited. In this study, the cat gene was identified in 69/192 (36%) R. anatipestifer isolated from different regions in China, including R. anatipestifer CH-2 that has been sequenced in previous study. Sequence analysis suggested that there are two copies of cat gene in this strain. Only both two copies of the cat mutant strain showed a significant decrease in resistance to chloramphenicol, exhibiting 4 μg/ml in the minimum inhibitory concentration for this antibiotic, but not for the single cat gene deletion strains. Functional analysis of the cat gene via expression in Escherichia coli BL21 (DE3) cells and in vitro site-directed mutagenesis indicated that His79 is the main catalytic residue of CAT in R. anatipestifer. These results suggested that chloramphenicol resistance of R. anatipestifer CH-2 is mediated by the cat genes. Finally, homology analysis of types A and B CATs indicate that R. anatipestifer comprises type B3 CATs.

Tetracycline and Phenicol Resistance Genes and Mechanisms: Importance for Agriculture, the Environment, and Humans

Recent reports have speculated on the future impact that antibiotic-resistant bacteria will have on food production, human health, and global economics. This review examines microbial resistance to tetracyclines and phenicols, antibiotics that are widely used in global food production. The mechanisms of resistance, mode of spread between agriculturally and human-impacted environments and ecosystems, distribution among bacteria, and the genes most likely to be associated with agricultural and environmental settings are included. Forty-six different tetracycline resistance () genes have been identified in 126 genera, with (M) having the broadest taxonomic distribution among all bacteria and (B) having the broadest coverage among the Gram-negative genera. Phenicol resistance genes are organized into 37 groups and have been identified in 70 bacterial genera. The review provides the latest information on tetracycline and phenicol resistance genes, including their association with mobile genetic elements in bacteria of environmental, medical, and veterinary relevance. Knowing what specific antibiotic-resistance genes (ARGs) are found in specific bacterial species and/or genera is critical when using a selective suite of ARGs for detection or surveillance studies. As detection methods move to molecular techniques, our knowledge about which type of bacteria carry which resistance gene(s) will become more important to ensure that the whole spectrum of bacteria are included in future surveillance studies. This review provides information needed to integrate the biology, taxonomy, and ecology of tetracycline- and phenicol-resistant bacteria and their resistance genes so that informative surveillance strategies can be developed and the correct genes selected.

Antimicrobial resistance genes in marine bacteria and human uropathogenic Escherichia coli from a region of intensive aquaculture

Antimicrobials are heavily used in Chilean salmon aquaculture. We previously found significant differences in antimicrobial-resistant bacteria between sediments from an aquaculture and a non-aquaculture site. We now show that levels of antimicrobial resistance genes (ARG) are significantly higher in antimicrobial-selected marine bacteria than in unselected bacteria from these sites. While ARG in tetracycline- and florfenicol-selected bacteria from aquaculture and non-aquaculture sites were equally frequent, there were significantly more plasmid-mediated quinolone resistance genes per bacterium and significantly higher numbers of qnrB genes in quinolone-selected bacteria from the aquaculture site. Quinolone-resistant urinary Escherichia coli from patients in the Chilean aquacultural region were significantly enriched for qnrB (including a novel qnrB gene), qnrS, qnrA and aac(6')-1b, compared with isolates from New York City. Sequences of qnrA1, qnrB1 and qnrS1 in quinolone-resistant Chilean E. coli and Chilean marine bacteria were identical, suggesting horizontal gene transfer between antimicrobial-resistant marine bacteria and human pathogens.

Sulfonamide and tetracycline resistance genes in total- and culturable-bacterial assemblages in South African aquatic environments

Antibiotic resistant bacteria are ubiquitous in the natural environment. The introduction of effluent derived antibiotic resistance genes (ARGs) into aquatic environments is of concern in the spreading of genetic risk. This study showed the prevalence of sulfonamide and tetracycline resistance genes, sul1, sul2, sul3, and tet(M), in the total bacterial assemblage and colony forming bacterial assemblage in river and estuarine water and sewage treatment plants (STP) in South Africa. There was no correlation between antibiotic concentrations and ARGs, suggesting the targeted ARGs are spread in a wide area without connection to selection pressure. Among sul genes, sul1 and sul2 were major genes in the total (over 10(-2) copies/16S) and colony forming bacteria assemblages (∼10(-1) copies/16S). In urban waters, the sul3 gene was mostly not detectable in total and culturable assemblages, suggesting sul3 is not abundant. tet(M) was found in natural assemblages with 10(-3) copies/16S level in STP, but was not detected in colony forming bacteria, suggesting the non-culturable (yet-to-be cultured) bacterial community in urban surface waters and STP effluent possess the tet(M) gene. Sulfamethoxazole (SMX) resistant (SMX(r)) and oxytetracycline (OTC) resistant (OTC(r)) bacterial communities in urban waters possessed not only sul1 and sul2 but also sul3 and tet(M) genes. These genes are widely distributed in SMX(r) and OTC(r) bacteria. In conclusion, urban river and estuarine water and STP effluent in the Durban area were highly contaminated with ARGs, and the yet-to-be cultured bacterial community may act as a non-visible ARG reservoir in certain situations.

Rapid electrochemical phenotypic profiling of antibiotic-resistant bacteria

Rapid phenotyping of bacteria to identify drug-resistant strains is an important capability for the treatment and management of infectious disease. At present, the rapid determination of antibiotic susceptibility is hindered by the requirement that, in existing devices, bacteria must be pre-cultured for 2-3 days to reach detectable levels. Here we report a novel electrochemical approach that achieves rapid readout of the antibiotic susceptibility profile of a bacterial infection within one hour. The electrochemical reduction of a redox-active molecule is monitored that reports on levels of metabolically-active bacteria. Bacteria are captured in miniaturized wells, incubated with antimicrobials and monitored for resistance. This electrochemical phenotyping approach is effective with clinically-relevant levels of bacteria, and provides results comparable to culture-based analysis. Results, however, are delivered on a much faster timescale, with resistance profiles available after a one hour incubation period.

Novel macrolide-resistance genes, mef(C) and mph(G), carried by plasmids from Vibrio and Photobacterium isolated from sediment and seawater of a coastal aquaculture site

The aim of this study was to determine whether mef(C) and mph(G), originally found on the transferable multi-drug plasmid pAQU1 from Photobacterium damselae subsp. damselae isolated from seawater of a fish farm, are responsible for conferring macrolide resistance. Since these genes are localized head-to-tail on pAQU1 and only four nucleotides exist between them, the single- and combination-effect of these genes was examined. When mph(G) alone was introduced to Escherichia coli, the minimum inhibitory concentrations (MICs) against erythromycin, clarithromycin and azithromycin increased, whereas introduction of mef(C) alone did not influence macrolide susceptibility. Introduction of both mef(C) and mph(G) dramatically increased the MICs to the same three macrolides, i.e. >512 μg ml(-1) , >512 μg ml(-1) and 128 μg ml(-1) respectively. These results suggest that the macrolide phosphotransferase encoded by mph(G) is essential for macrolide resistance, while the efflux pump encoded by mef(C) is required for high-level macrolide resistance. The tandem-pair arrangements of the mef(C) and mph(G) genes were conserved on plasmids ranging in size from 240 to 350 kb of the 22 erythromycin-resistant strains belonging to Vibrio and Photobacterium obtained from the fish farm. Sixteen of 22 plasmids ranged in size from 300 to 350 kb. This is the first report of novel macrolide resistance genes originating from a marine bacterium.

SIGNIFICANCE AND IMPACT OF THE STUDY

In this study, mef(C) and mph(G) were found to be novel macrolide-resistance genes, and this is the first report of macrolide-resistance genes originating from a marine bacterium. These genes may be responsible for previously reported cases of the emergence of erythromycin-resistant bacteria in aquaculture sites by an unknown mechanism. The introduction of the tandem arrangement of the mef(C) and mph(G) genes in Escherichia coli increased the MICs to erythromycin, clarithromycin and azithromycin, suggesting a novel mechanism conferring high-level macrolide resistance via combined expression of the efflux pump and macrolide phosphotransferase.

Seasonal variability in airborne biotic contaminants in swine confinement buildings

Little is known about the seasonal dynamics of biotic contaminants in swine confinement buildings (SCBs). The biotic contaminants of seven SCBs were monitored during one visit in the winter and one during the summer. Paired-end Illumina sequencing of the 16S rRNA gene, V3 region, was used to examine seasonal shifts in bacterial community composition and diversity. The abundances of 16S rRNA genes and six tetracycline resistance genes (tetB, tetH, tetZ, tetO, tetQ, and tetW) were also quantified using real-time PCR. Bacterial abundances, community composition and diversity all showed strong seasonal patterns defined by winter peaks in abundance and diversity. Microclimatic variables of SCBs, particularly air speed, PM2.5 and total suspended particles (TSP) were found significantly correlated to abundances, community composition, and diversity of bacterial bioaerosols. Seasonal fluctuations were also observed for four tetracycline resistance genes, tetH, tetO, tetQ, and tetW. The frequency of occurrences of these resistance genes were significantly higher in samples collected during winter and was also significantly correlated with air speed, PM2.5 and TSP. Overall, our results indicate that biotic contaminants in SCBs exhibit seasonal trends, and these could be associated with the microclimatic variables of SCBs. The correlations established in the current study could be helpful in establishing better management strategies to minimize the potential health impacts on both livestock and humans working in this environment.

Co-resistance to different classes of antibiotics among ESBL-producers from aquatic systems

In this study we investigated the co-occurrence of resistance to non-beta-lactams among cefotaxime-resistant extended-spectrum beta-lactamase (ESBL) producers (ESBL(+)) versus non-ESBL producers (ESBL(-)), from aquatic environments. Higher prevalence of resistance to tetracycline, fluoroquinolones and aminoglycosides were observed in ESBL(+). Among ESBL(+) resistant to tetracycline (n = 18), tet(A) was detected in 88.9% and tet(B) in 16.7%. Among fluoroquinolone-resistant-ESBL(+) (n = 15), aacA4-cr and qnrVC4 were identified in 26.6% and 40% strains, respectively. The qnrVC4 gene was detected for the first time in Pseudomonas sp. and Escherichia coli. Class 1 integrase genes were detected in 56.41% of ESBL(+) and in 27.67% ESBL(-). Gene cassette arrays identified conferred resistance to aminoglycosides (aadA-type genes and aacA4), trimethoprim (dfrA17), chloramphenicol (catB8), fluoroquinolones (qnrVC4) and beta-lactams (blaOXA-10). Conjugation experiments were performed with CTX-M-producers. Transconjugants showed multiresistance to 3 or more classes of antibiotics, and conjugative plasmids were assigned to IncF, IncK and IncI1 replicons. Results obtained showed that co-selection of resistance to aminoglycosides, quinolones and tetracyclines is prevalent among ESBL-producers and that these features are successfully mobilized by IncF, IncK and IncI1 conjugative plasmids. This study reinforces the importance of natural aquatic systems as reservoir of mobile genetic platforms carrying multiple resistance determinants. Moreover, to the best of our knowledge, this constitutes the first observation of IncK::CTX-M-3 in Aeromonas hydrophila and the first report of IncK plasmids in Portugal.

Mechanisms of antimicrobial resistance in finfish aquaculture environments

Consumer demand for affordable fish drives the ever-growing global aquaculture industry. The intensification and expansion of culture conditions in the production of several finfish species has been coupled with an increase in bacterial fish disease and the need for treatment with antimicrobials. Understanding the molecular mechanisms of antimicrobial resistance prevalent in aquaculture environments is important to design effective disease treatment strategies, to prioritize the use and registration of antimicrobials for aquaculture use, and to assess and minimize potential risks to public health. In this brief article we provide an overview of the molecular mechanisms of antimicrobial resistance in genes found in finfish aquaculture environments and highlight specific research that should provide the basis of sound, science-based policies for the use of antimicrobials in aquaculture.

Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health

The worldwide growth of aquaculture has been accompanied by a rapid increase in therapeutic and prophylactic usage of antimicrobials including those important in human therapeutics. Approximately 80% of antimicrobials used in aquaculture enter the environment with their activity intact where they select for bacteria whose resistance arises from mutations or more importantly, from mobile genetic elements containing multiple resistance determinants transmissible to other bacteria. Such selection alters biodiversity in aquatic environments and the normal flora of fish and shellfish. The commonality of the mobilome (the total of all mobile genetic elements in a genome) between aquatic and terrestrial bacteria together with the presence of residual antimicrobials, biofilms, and high concentrations of bacteriophages where the aquatic environment may also be contaminated with pathogens of human and animal origin can stimulate exchange of genetic information between aquatic and terrestrial bacteria. Several recently found genetic elements and resistance determinants for quinolones, tetracyclines, and β-lactamases are shared between aquatic bacteria, fish pathogens, and human pathogens, and appear to have originated in aquatic bacteria. Excessive use of antimicrobials in aquaculture can thus potentially negatively impact animal and human health as well as the aquatic environment and should be better assessed and regulated.

Limited diversity in the gene pool allows prediction of third-generation cephalosporin and aminoglycoside resistance in Escherichia coli and Klebsiella pneumoniae

Early appropriate antibiotic treatment reduces mortality in severe sepsis, but current methods to identify antibiotic resistance still generally rely on bacterial culture. Modern diagnostics promise rapid gene detection, but the apparent diversity of relevant resistance genes in Enterobacteriaceae is a problem. Local surveys and analysis of publicly available data sets suggested that the resistance gene pool is dominated by a relatively small subset of genes, with a very high positive predictive value for phenotype. In this study, 152 Escherichia coli and 115 Klebsiella pneumoniae consecutive isolates with a cefotaxime, ceftriaxone and/or ceftazidime minimum inhibitory concentration (MIC) of ≥ 2 μg/mL were collected from seven major hospitals in Sydney (Australia) in 2008-2009. Nearly all of those with a MIC in excess of European Committee on Antimicrobial Susceptibility Testing (EUCAST) resistance breakpoints contained one or more representatives of only seven gene types capable of explaining this phenotype, and this included 96% of those with a MIC ≥ 2 μg/mL to any one of these drugs. Similarly, 97% of associated gentamicin-non-susceptibility (MIC ≥ 8 μg/mL) could be explained by three gene types. In a country like Australia, with a background prevalence of resistance to third-generation cephalosporins of 5-10%, this equates to a negative predictive value of >99.5% for non-susceptibility and is therefore suitable for diagnostic application. This is an important proof-of-principle that should be tested in other geographic locations.