Survey Of Antimicrobial Resistance Research Articles

Technical specifications for a EU-wide baseline survey of antimicrobial resistance in bacteria from aquaculture animals.

The European Commission requested scientific and technical assistance in the preparation of a EU-wide baseline survey of antimicrobial resistance (AMR) in bacteria from aquaculture animals. It is recommended that the survey would aim at estimating the occurrence of AMR in Aeromonas spp. isolated from Atlantic Salmon (Salmo salar), European seabass (Dicentrarchus labrax) and trout (Salmo trutta, Salvelinus fontinalis, Oncorhynchus mykiss) intended to consumption, at harvesting (at farm/slaughter), at the EU level and in addition, at estimating the occurrence and diversity of AMR of Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Vibrio parahaemolyticus and Vibrio alginolyticus in blue mussel (Mytilus edulis) and Mediterranean mussel (Mytilus galloprovincialis) from production areas and at dispatch centres at the EU level. These technical specifications define the target populations, the sample size for the survey, sample collection requirements, the analytical methods (for isolation, identification, phenotypic susceptibility testing and further genotypic analysis of some of the bacteria targeted) and the data reporting requirements. The data to be reported by the EU Member States to support this baseline survey are presented in three data models. The results of the survey should be reported using the EFSA reporting system.

Development of a High-Throughput Analytical Method for Antimicrobials in Wastewater Using an Automated Pipetting and Solid-Phase Extraction System.

Antimicrobial resistance (AMR) has emerged and spread globally. Recent studies have also reported the presence of antimicrobials in a wide variety of aquatic environments. Conducting a nationwide monitoring survey of AMR in the environment to elucidate its status and to assess its impact on ecosystems and human health is of social importance. In this study, we developed a novel high-throughput analysis (HTA) system based on a 96-well plate solid-phase extraction (SPE), using automated pipetting and an SPE pre-treatment system. The effectiveness of the system as an HTA for antimicrobials in environmental water was verified by comparing it with a conventional manual analytical system in a domestic hospital over a period of two years and four months. The results of the manual analysis and HTA using a combination of automated pipetting and SPE systems were generally consistent, and no statistically significant difference was observed (p > 0.05) between the two systems. The agreement ratios between the measured concentrations based on the conventional and HTA methods were positively correlated with a correlation coefficient of r = 0.99. These results indicate that HTA, which combines automated pipetting and an SPE pre-treatment system for rapid, high-volume analysis, can be used as an effective approach for understanding the environmental contamination of antimicrobials at multiple sites. To the best of our knowledge, this is the first report to present the accuracy and agreement between concentrations based on a manual analysis and those measured using HTA in hospital wastewater. These findings contribute to a comprehensive understanding of antimicrobials in aquatic environments and assess the ecological and human health risks associated with antimicrobials and antimicrobial-resistant bacteria to maintain the safety of aquatic environments.

Antimicrobial resistance survey and whole-genome analysis of nosocomial P. Aeruginosa isolated from eastern Province of China in 2016–2021

BackgroundPseudomonas aeruginosa is a major Gram-negative pathogen that can exacerbate lung infections in the patients with cystic fibrosis, which can ultimately lead to death.MethodsFrom 2016 to 2021, 103 strains of P. aeruginosa were isolated from hospitals and 20 antibiotics were used for antimicrobial susceptibility determination. Using next-generation genome sequencing technology, these strains were sequenced and analyzed in terms of serotypes, ST types, and resistance genes for epidemiological investigation.ResultsThe age distribution of patients ranged from 10 days to 94 years with a median age of 69 years old. The strains were mainly isolated from sputum (72 strains, 69.9%) and blood (14 strains, 13.6%). The size of these genomes ranged from 6.2 Mb to 7.4 Mb, with a mean value of 6.5 Mb. In addition to eight antibiotics that show inherent resistance to P. aeruginosa, the sensitivity rates for colistin, amikacin, gentamicin, ceftazidime, piperacillin, piperacillin-tazobactam, ciprofloxacin, meropenem, aztreonam, imipenem, cefepime and levofloxacin were 100%, 95.15%, 86.41%, 72.82%, 71.84%, 69.90%, 55.34%, 52.43%, 50.49%, 50.49%, 49.51% and 47.57% respectively, and the carriage rate of MDR strains was 30.69% (31/101). Whole-genome analysis showed that a total of 50 ST types were identified, with ST244 (5/103) and ST1076 (4/103) having a more pronounced distribution advantage. Serotype predictions showed that O6 accounted for 29.13% (30/103), O11 for 23.30% (24/103), O2 for 18.45% (19/103), and O1 for 11.65% (12/103) of the highest proportions. Notably, we found a significantly higher proportion of ExoU in P. aeruginosa strains of serotype O11 than in other cytotoxic exoenzyme positive strains. In addition to this, a total of 47 crpP genes that mediate resistance to fluoroquinolones antibiotics were found distributed on 43 P. aeruginosa strains, and 10 new variants of CrpP were identified, named 1.33, 1.34, 1.35, 1.36, 1.37, 1.38, 1.39, 1.40, 1.41 and 7.1.ConclusionsWe investigated the antibiotic susceptibility of clinical isolates of P. aeruginosa and genomically enriched the diversity of P. aeruginosa for its prophylactic and therapeutic value.

Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact.

Here, we examine surface waters as a modality to better understand baseline antimicrobial resistance (AMR) across the environment to supplement existing AMR monitoring in pathogens associated with humans, foods, and animals. Data from metagenomic and quasimetagenomic (shotgun sequenced enrichments) are used to describe AMR in Maryland surface waters from high and low human impact classifications.

Risk of zoonoses involving slow-growing non-tuberculous mycobacteria: Survey of antimicrobial resistance among strains from domestic and wild animals

Non-tuberculous mycobacteria are opportunistic pathogens that cause disease mainly in immunocompromised hosts. The present study assessed the prevalence of antibiotic resistance among such mycobacteria from domestic and wild animals in Croatia sampled during several years within a national surveillance program. A total of 44 isolates belonging to nine slow-growing species were genotyped and analyzed for susceptibility to 13 antimicrobials often used to treat non-tuberculous mycobacterial infections in humans. Most prevalent resistance was to moxifloxacin (77.3%), doxycycline (76.9%), and rifampicin (76.9%), followed by ciprofloxacin (65.4%), trimethoprim-sulfamethoxazole (65.4%), and linezolid (61.4%). Few isolates were resistant to rifabutin (7.7%) or amikacin (6.8%). None of the isolates was resistant to clarithromycin. Nearly all isolates (86.4%) were resistant to multiple antibiotics. Our findings suggest substantial risk that human populations may experience zoonotic infections with non-tuberculous mycobacteria that will be difficult to treat using the current generation of antibiotics. Future work should clarify how resistance emerges in wild populations of non-tuberculous mycobacteria.

The Pattern of Antimicrobial Prescription at a Tertiary Health Center in Egypt: A Point Survey and Implications

The misuse of antimicrobials has major consequences, particularly antimicrobial resistance (AMR) and antimicrobials' related adverse effects. So, the WHO proposed antimicrobial surveillance to improve antimicrobials use. This point prevalence survey (PPS) was conducted to illustrate the prevalence of antimicrobial use at Mansoura University hospitals (MUH), Egypt. The survey process used was adapted from the European survey of antimicrobial resistance with modifications. The survey was conducted from 8 AM to 8 PM daily within 2 weeks. A total of 300 patients received antimicrobials and the prevalence rate of antimicrobial prescription was 79.15%. The major indications of antimicrobials were surgical prophylaxis followed by the treatment of community-acquired infection. The most commonly prescribed initial antimicrobial group was Aminopenicillin ± β-lactamase inhibitors. Although the purpose for antimicrobial administration was recorded in all cases, the stop/review history was recorded only in 19.6% and local guidelines were not available for 77.6% of antimicrobial prescriptions. The use of combined antimicrobials was common (46.6%), particularly in orthopedic and cardiothoracic surgery. The prevalence of antimicrobial prescription at MUH was high which requires serious actions including reviewing the antimicrobial indication, implementing local prescription guidelines, initiating an antimicrobial stewardship program (ASP), and optimizing infection control measures.

Antimicrobial Susceptibility Survey of Invasive Haemophilus influenzae in the United States in 2016.

ABSTRACTAntibiotics are important for the treatment and prevention of invasive Haemophilus influenzae disease. Reduced susceptibility to clinically relevant drugs, except ampicillin, has been uncommon in the United States. Susceptibility of 700 invasive H. influenzae isolates, collected through population-based surveillance during 2016, was assessed for 15 antibiotics using broth microdilution, according to the CLSI guidelines; a subset of 104 isolates were also assessed for rifampin susceptibility using Etest. Genomes were sequenced to identify genes and mutations known to be associated with reduced susceptibility to clinically relevant drugs. A total of 508 (72.6%) had reduced susceptibility to at least one antibiotic and more than half of the isolates exhibited reduced susceptibility to only one (33.6%) or two (21.6%) antibiotic classes. All tested isolates were susceptible to rifampin, a chemoprophylaxis agent, and <1% (n = 3) of isolates had reduced susceptibility to third generation cephalosporins, which are recommended for invasive disease treatment. In contrast, ampicillin resistance was more common (28.1%) and predominantly associated with the detection of a β-lactamase gene; 26.2% of isolates in the collection contained either a TEM-1 or ROB-1 β-lactamase gene, including 88.8% of ampicillin-resistant isolates. β-lactamase negative ampicillin-resistant (BLNAR) isolates were less common and associated with ftsI mutations; resistance to amoxicillin-clavulanate was detected in <2% (n = 13) of isolates. The proportion of reduced susceptibility observed was higher among nontypeable H. influenzae and serotype e than other serotypes. US invasive H. influenzae isolates remain predominantly susceptible to clinically relevant antibiotics except ampicillin, and BLNAR isolates remain uncommon.IMPORTANCE Antibiotics play an important role for the treatment and prevention of invasive Haemophilus influenzae disease. Antimicrobial resistance survey of invasive H. influenzae isolates collected in 2016 showed that the US H. influenzae population remained susceptible to clinically relevant antibiotics, except for ampicillin. Detection of approximately a quarter ampicillin-resistant and β-lactamase containing strains demonstrates that resistance mechanisms can be acquired and sustained within the H. influenzae population, highlighting the continued importance of antimicrobial resistance surveillance for H. influenzae to monitor susceptibility trends and mechanisms of resistance.

Spatiotemporal distribution of antimicrobial resistant organisms in different water environments in urban and rural settings of Bangladesh

The spatial distribution of clinically important antibiotic resistant bacteria (ARB) and associated genes is important to identify the environmental distribution of contamination and ‘hotspots’ of antimicrobial resistance (AMR). We conducted an integrated survey of AMR in drinking water, wastewater and surface water (rivers and ponds) in three settings in Bangladesh: rural households, rural poultry farms, and urban food markets. Spatial mapping was conducted via geographic information system (GIS) using ArcGIS software. Samples (n = 397) were analyzed for the presence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec), carbapenem-resistant E. coli (CR-Ec) and resistance genes (blaCTX-M-1,blaNDM-1). In rural households, 5% of drinking water supply samples tested positive for ESBL-Ec, and a high proportion of wastewater, pond and river water samples were positive for ESBL-Ec (90%, 76%, and 85%, respectively). In poultry farms, 10% of drinking water samples tested positive for ESBL-Ec compared to a high prevalence in wastewater, pond and river water (90%, 68%, and 85%, respectively). CR-Ec prevalence in household wastewater and pond water was relatively low (8% and 5%, respectively) compared to river water (33%). In urban areas, 38% of drinking water samples and 98% of wastewater samples from food markets tested positive for ESBL-Ec while 30% of wastewater samples tested positive for CR-Ec. Wastewaters had the highest concentrations of ESBL-Ec, CR-Ec, blaCTXM-1 and blaNDM-1 and these were significantly higher in urban compared to rural samples (p < 0.05). ESBL-Ec is ubiquitous in drinking water, wastewater and surface water bodies in both rural and urban areas of Bangladesh. CR-Ec is less widespread but found at a high prevalence in wastewater discharged from urban food markets and in rural river samples. Surveillance and monitoring of antibiotic resistant organisms and genes in waterbodies is an important first step in addressing environmental dimensions of AMR.

The Associations between Poor Antibiotic and Antimicrobial Resistance Knowledge and Inappropriate Antibiotic Use in the General Population Are Modified by Age.

Objectives: Understanding factors influencing inappropriate antibiotic use can guide the design of interventions to improve antibiotic practices and reduce antimicrobial resistance (AMR). Methods: A nationally representative cross-sectional survey (N = 2004) was conducted between November 2020 and January 2021. Knowledge of antibiotic use and AMR using the World Health Organization’s Multi-Country AMR Survey questionnaire, and antibiotic practices were examined. Multivariable logistic regression was performed to identify factors associated with inappropriate antibiotic use and examine effect measure modifications. Results: After adjusting for potential confounding, poor knowledge of antibiotic use was associated with a 3x increased odds of inappropriate antibiotic use in adults aged ≥50 years (aOR 3.11, 95% CI [2.24–4.32]), 5× increased odds in those aged 35–49 years (aOR 4.88, 95% CI [3.32–7.16]), and 7× increased odds in those aged 21–34 years (aOR 6.58, 95% CI [4.19–10.33]). While there was no statistically significant association in adults aged ≥50 years, poor knowledge of AMR increased the odds of inappropriate antibiotic use by 4 times in adults aged 35–49 years (aOR 3.73, 95% CI [1.53–9.11]) and 5 times in those aged 21–34 years (aOR 4.90, 95% CI [1.84–13.02]). Conclusions: Targeted educational interventions for specific age groups are needed in conjunction with empowering the public with knowledge of antibiotic use and AMR.

A four-year follow-up survey of antimicrobial resistance among Acinetobacter baumannii complex from inpatients in Southern Brazil

Objectives: To determine the trends of antimicrobial resistance for Acinetobacter baumannii complex isolates recovered from inpatients over a 4-year follow-up survey. Methods: A total of 659 A baumannii complex isolates were recovered from hospitalized patients in Porto Alegre and its metropolitan area, Southern Brazil, from 2017 to 2020. Susceptibility profile was determined for ampicillin/sulbactam, amikacin, gentamicin, imipenem, meropenem, minocycline, polymyxin B and tigecycline. Results: Overall, PMB was the most active agent against the set of A baumannii isolates over the period. Although stable, a high resistance rate was observed. Conclusions: Our results shown the presence of an extensively-drug resistant A baumannii complex isolates over the past four years. Polymyxin B has been the only antimicrobial agent that remain with a good in vitro activity. Strict surveillance and infection control measures are mandatory.

Knowledge, attitude and practice on antibiotic use and resistance among the Italian population, 2019

Abstract Background Public knowledge, awareness and behaviors related to antibiotic use and antimicrobial-resistance (AMR) are vital to ensure the prudent use of these drugs. In this work, we present the top-line results of the first national survey of AMR among the Italian general population aged ≥18 years. Methods From August to September 2019, we conducted a population-based cross-sectional random survey through mixed CATI/CAMI/CAWI methodologies among representative samples of the general population, parents of children aged 0-11 years, adults ≥65 years and pet's owners. Results were summarized using relative frequencies. Results Of 1,400 persons interviewed, 47% and 68% respectively correctly said that it is false that antibiotics kill viruses and are effective at treating colds and flu. More than 80% of respondents considered themselves to be well-informed about antibiotics but only one in two people knew what is meant by AMR. While the vast majority (96%) of respondents said that they obtained the last course of antibiotics that they used from a medical prescription, 11% incorrectly said that they stopped taking antibiotics when they felt better or that they used those left over from a previous course. In addition, 55% of pet's owners said they obtained antibiotics without a prescription from a pharmacy or elsewhere. Almost all respondents (97%) believed that it's everyone's responsibility to use antibiotics wisely, with the 80% who expressed concerns about the potential of AMR to affect themselves and their families; however, 40% did not think that action at an individual level is the most effective way of tackling resistance to antibiotics. Conclusions Our findings show some improvement in Italians' knowledge, awareness and behaviors related to antibiotic use and AMR but there are needs to be a greater sense of responsibility to take charge of the AMR problem. These results may be drivers of structured national awareness campaigns. Key messages In 2019, we conducted the first national survey of AMR among the Italian population: &amp;gt;80% of respondents felt themselves well-informed about antibiotics but only 1/2 people knew what is meant by AMR. Almost all Italian sample believed that it's everyone's responsibility to use antibiotics wisely, but 40% did not think that action at an individual level is effective to tackle AMR.

The Use of Sheep Movement Data to Inform Design and Interpretation of Slaughterhouse-Based Surveillance Activities.

The design of surveillance strategies is often a compromise between science, feasibility, and available resources, especially when sampling is based at fixed locations, such as slaughter-houses. Advances in animal identification, movement recording and traceability should provide data that can facilitate the development, design and interpretation of surveillance activities. Here, for the first time since the introduction of electronic identification of sheep, the utility of a statutory sheep movement database to inform the design and interpretation of slaughter-house based surveillance activities has been investigated. Scottish sheep movement records for 2015–2018 were analyzed in combination with several other data sources. Patterns of off-farm movements of Scottish sheep to slaughter were described and the spatial distribution of several distinct slaughter populations, throughputs and catchment areas for Scottish slaughterhouses were determined. These were used to evaluate the coverage of a convenience-sample slaughter-house based survey for antimicrobial resistance (AMR). In addition, non-slaughter sheep movements within and between Scottish regions were described and inter-and intra-regional movement matrices were produced. There is potential at a number of levels for bias in spatially-associated factors for ovine surveillance activities based at Scottish slaughterhouses. The first is intrinsic because the slaughtered in Scotland population differs from the overall Scottish sheep slaughter population. Other levels will be survey-dependent and occur when the catchment area differs from the slaughtered in Scotland population and when the sampled sheep differ from the catchment area. These are both observed in the AMR survey. Furthermore, the Scottish non-slaughter sheep population is dynamic. Inter-regional movements vary seasonally, driven by the sheep calendar year, structure of the Scottish sheep industry and management practices. These sheep movement data provide a valuable resource for surveillance purposes, despite a number of challenges and limitations that were encountered. They can be used to identify and characterize the spatial origin of relevant populations and so inform the interpretation of existing slaughterhouse-based surveillance activities. They can be used to improve future design by exploring the feasibility and cost:benefit of alternative sampling strategies. Further development could also contribute to other surveillance activities, such as situational awareness and resource allocation, for the benefit of stakeholders.

Leprosy: current status and clinical management

Abstract Around the world nations have adopted the global leprosy strategy 2016–2020 developed by the world health organization to achieve the objective of a leprosy-free world. Despite the disease having been declared as eliminated from most developed nations and parts of the world, every year more than 2,00,000 new cases of leprosy still continue to occur mainly in south east Asian regions (India, Indonesia, Philippines) and south American region of Brazil. The diagnosis of leprosy has remained more or less the same over the years with recent advances in the form of PCR-based molecular diagnosis and immunological markers. Much of the success of national programs have been due to multi-drug therapy. Recently, anti-microbial resistance surveys have shown the need to monitor for drug resistance in leprosy. The countries where the disease is still endemic need to shift their policy towards active surveillance and case finding in the affected districts. We are in the last year of the Global Leprosy Strategy 2016–2020 by WHO: accelerating towards a Leprosy free world, but eradication of the disease seems a distant possibility as of now.

A survey of antimicrobial resistance in Enterobacteriaceae isolated from the Chesapeake Bay and adjacent upper tributaries.

In recent years, the rise in antimicrobial resistance (AR) in the healthcare setting as well as the environment has been recognized as a growing public health problem. The Chesapeake Bay (CB) and its upper tributaries (UT) is a large and biologically diverse estuary. This pilot study evaluated the presence of AR of gram‐negative bacteria isolated from water samples collected at various sites of the Chesapeake Bay. Bacterial organisms were identified and antimicrobial susceptibility testing was performed by phenotypic and genotypic methods. Ninety‐two distinctly different gram‐negative bacteria were identified; Klebsiella pneumoniae, Enterobacter cloacae, Enterobacter aerogenes, Serratia marcescens, and Escherichia coli were most often isolated. Serratia marcescens was more frequently isolated in samples from the UT compared to the CB. Antimicrobial resistance was more frequently detected in organisms from the CB by phenotypic and genotypic methods. Antimicrobial resistance to ampicillin, imipenem, tetracycline, and chloramphenicol were the most frequently observed resistance patterns. ACT‐1, CMY, and SHV genes were the most frequently detected resistance genes, with predominance in organism isolated from the CB. The results from this study emphasize the importance for further developing comprehensive surveillance programs of AR in bacterial isolates in the various environments, such as recreational and other water systems.

Demographic, Knowledge and Impact Analysis of 57,627 Antibiotic Guardians Who Have Pledged to Contribute to Tackling Antimicrobial Resistance.

In 2014, Public Health England (PHE) developed the behavioural change Antibiotic Guardian (AG) campaign to tackle antimicrobial resistance (AMR). This included an online pledge system aimed at healthcare professionals (HCP) and the public. Demographics of AGs were collected when pledging online and analysed by pledge group, type, geography, and source of hearing of the campaign between 24/07/2014–31/12/2017. Website visitors and acquisition routes were described using Google analytics data. From November 2016, five questions assessed AMR knowledge which was compared to published Eurobarometer AMR survey results for UK. Behaviour change of AGs was also assessed through an impact questionnaire, evaluating the effect of the campaign on self-reported behaviour around AMR. Overall there were 231,460 unique website visitors from 202 countries resulting in 57,627 English and 652 foreign language pledges. Website visitors increased each year with peaks during European Antibiotic Awareness Day and (EAAD) World Antibiotic Awareness Week (WAAW). Self-direction was the largest acquisition route (55%) with pledges more likely via this route than social media (OR 2.6, 95% CI 2.5–2.6). AGs (including the public) were more likely to answer questions correctly than the Eurobarometer UK group (OR 8.5, 95% CI 7.4–9.9). AG campaign engagement has increased over the four years with particular increases in the student group. AGs had greater knowledge compared to the Eurobarometer UK population. The latest impact evaluation of the online pledge scheme highlights that it continues to be an effective and inexpensive way to engage people with the problem of AMR especially among those with prior awareness of the topic.

Whole-genome sequences of multidrug-resistant Escherichia coli in South-Kivu Province, Democratic Republic of Congo: characterization of phylogenomic changes, virulence and resistance genes

BackgroundExtended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are responsible for severe infections worldwide. Whereas their genotypic and pathogenic characteristics are not documented in Democratic Republic of Congo (DRC), recent studies conducted at the Bukavu General Hospital in the South Kivu province highlighted their high prevalence in extra-intestinal infections. Here we provide data on molecular characterization of ESBL producing-Escherichia coli isolates from patients with extra-intestinal infections at this provincial hospital.MethodsWhole-genome sequencing was carried out on 21 of these ESBL-producing Extra-intestinal Pathogenic Escherichia coli (ExPEC) for analysis of phylogenomic evolution, virulence factor and antimicrobial resistance (AMR) genes. Data were compared to phylogenetically close genomes using Multi-Locus Sequence Typing and Single Nucleotide Polymorphism-based phylogenetic approaches.ResultsThe distribution of E. coli sequence types (ST) was as follows: ST 131 (n = 7), ST405 (n = 4), ST410 (n = 2), and other STs (ST10, ST58, ST95, ST393, ST443, S617, ST648, and ST2450). All ST131 belonged to the O25b-ST131 pandemic clone. Unexpectedly, they harbored more virulence genes than their GenBank counterparts. IncF plasmid replicons included novel FIB 69, FII 105 and FII 107 alleles. ESBL-genes included the plasmid-mediated CTX-M-15 in all isolates, and the SHV-12 allele. Other AMR genes included blaOXA-1, blaTEM-1, as well as genes encoding resistance against aminoglycosides, quinolones, chloramphenicol, rifampicin, tetracyclines, sulfonamides and trimethoprim.ConclusionCurrent data confirm the clonal spread of ESBL-producing ST131 and ST405 clones in patients from South Kivu, and the acquisition of resistance and virulence genes. A closer survey of AMR and virulence should therefore be prompted in this high-risk area.

High prevalence of carriage of mcr-1-positive enteric bacteria among healthy children from rural communities in the Chaco region, Bolivia, September to October 2016.

BackgroundThe mcr-1 gene is a transferable resistance determinant against colistin, a last-resort antimicrobial for infections caused by multi-resistant Gram-negatives.AimTo study carriage of antibiotic-resistant bacteria in healthy school children as part of a helminth control and antimicrobial resistance survey in the Bolivian Chaco region.MethodsFrom September to October 2016 we collected faecal samples from healthy children in eight rural villages. Samples were screened for mcr-1- and mcr-2 genes. Antimicrobial susceptibility testing was performed, and a subset of 18 isolates representative of individuals from different villages was analysed by whole genome sequencing (WGS).ResultsWe included 337 children (mean age: 9.2 years, range: 7–11; 53% females). The proportion of mcr-1 carriers was high (38.3%) and present in all villages; only four children had previous antibiotic exposure. One or more mcr-1-positive isolates were recovered from 129 positive samples, yielding a total of 173 isolates (171 Escherichia coli, 1 Citrobacter europaeus, 1 Enterobacter hormaechei). No mcr-2 was detected. Co-resistance to other antimicrobials varied in mcr-positive E. coli. All 171 isolates were susceptible to carbapenems and tigecycline; 41 (24.0%) were extended-spectrum β-lactamase producers and most of them (37/41) carried bla CTX-M-type genes. WGS revealed heterogeneity of clonal lineages and mcr-genetic supports.ConclusionThis high prevalence of mcr-1-like carriage, in absence of professional exposure, is unexpected. Its extent at the national level should be investigated with priority. Possible causes should be studied; they may include unrestricted use of colistin in veterinary medicine and animal breeding, and importation of mcr-1-positive bacteria via food and animals.

Current and future antimicrobial resistance issues for the Australian pig industry

Antimicrobial use and antimicrobial resistance (AMR) in intensive pig production and its potential impacts to human and animal health are very much under the spotlight, both internationally, and within Australia. While the majority of AMR of medical importance is associated with the exclusive use of antimicrobials in humans, resistance in zoonotic foodborne pathogens such as Salmonella and Campylobacter, and livestock commensal bacteria such as Escherichia coli and Enterococcus spp., is under increased scrutiny. This is primarily due to the current reliance on many of the same drug classes as used in human medicine for treatment and control of bacterial diseases of livestock. Furthermore, the development of multidrug resistance in pathogens such as enterotoxigenic E. coli may drive off-label use of critically important drug classes such as 3rd-generation cephalosporins. This could lead to the emergence and amplification of resistance genes of potential public health significance in both pathogens and commensal bacteria. Livestock-associated and community-associated methicillin-resistant Staphylococcus aureus has also recently been detected in Australian pigs as a result of human-to-animal transmission and are a potential public health issue for in-contact piggery workers. Australia is in a unique position compared with many of its international trading partners due to its isolation, ban on importation of livestock and conservative approach to antimicrobial registration, including reservation of the fluoroquinolone class for use in humans and companion animals only. Cross-sectional AMR surveys of pathogens and commensals in healthy pigs have identified only low frequency of resistance to critically important drug classes. Nevertheless, resistance to critically important antimicrobials has emerged and careful antimicrobial stewardship is required to ensure that these low levels do not increase. In this report, we review AMR of significance to the Australian pig industry and identify potential prevention and control measures.

Characterization of resistance to tetracyclines and aminoglycosides of sheep mastitis pathogens: study of the effect of gene content on resistance.

Mastitis causes economic losses and antimicrobials are frequently used for mastitis treatment. Antimicrobial resistance surveys are still rare in the ovine field and characterization of strains is important in order to acquire information about resistance and for optimization of therapy. Bacterial pathogens recovered in milk samples from mastitis-affected ewes were characterized for resistance to tetracyclines and aminoglycosides, members of which are frequently used antimicrobials in small ruminants. A total of 185 strains of staphylococci, streptococci, and enterococci, common mastitis pathogens, were tested for minimal inhibitory concentration (MIC) to tetracycline, doxycycline, minocycline, gentamicin, kanamycin, streptomycin, and for resistance genes by PCR. Effects of different tet genes arrangements on MICs were also investigated. Staphylococci expressed the lowest MIC for tetracycline and tet(K) was the most common gene recovered; tet(M) and tet(O) were also found. Gene content was shown to influence the tetracycline MIC values. Enterococci and streptococci showed higher MICs to tetracyclines and nonsusceptible strains always harboured at least one ribosomal protection gene (MIC above 8μgml(-1) ). Streptococci often harboured two or more tet determinants. As regards the resistance to aminoglycosides, staphylococci showed the lowest gentamicin and kanamycin median MIC along with streptomycin high level resistant (HLR) strains (MIC >1024μgml(-1) ) all harbouring str gene. The resistance determinant aac(6')-Ie-aph(2″)-Ia was present in few strains. Streptococci were basically nonsusceptible to aminoglycosides but neither HLR isolates nor resistance genes were detected. Enterococci revealed the highest MICs for gentamicin; two str harbouring isolates were shown to be HLR to streptomycin. Evidence was obtained for the circulation of antimicrobial-resistant strains and genes in sheep dairy farming. Tetracycline MIC of 64μgml(-1) and high-level resistance were detected for streptomycin (MIC >1024μgml(-1) ), so that effectiveness of common treatments may be at risk.

Helicobacter pylori resistance to antibiotics in 2014 in France detected by phenotypic and genotypic methods

A large survey of antimicrobial resistance of Helicobacter pylori was performed in France in 2014: 984 patients were enrolled by 75 gastroenterologists all over the country. Among the 783 patients who had never received eradication treatment before, 266 (33.9%) were H. pylori positive. The strains showed a high rate of clarithromycin resistance (22.2%), moderate rate of resistance to levofloxacin (15.4%) and high rate of resistance to metronidazole (45.9%). In all, 187 patients had received previous treatment, of which 115 were H. pylori positive with very high resistance to clarithromycin (73.9%) and metronidazole (78.3%). None of the patients receiving PYLERA (Bismuth salt-Tetracycline HCl-Metronidazole) proton-pump inhibitor developed resistance to tetracycline. A real-time PCR applied to gastric biopsy specimens detected all the cases that were positive by culture as well as 30 additional cases. A good correlation was found between the clarithromycin resistance detected by phenotypic methods and the associated mutations for clarithromycin resistance, which has continued to increase in the last decade but at a lower rate than previously observed.