Resistance Surveillance Program Research Articles

Antibiotic Resistance Among Ocular Bacterial Pathogens from Pediatric Patients: Ten-Year Results from the ARMOR Surveillance Study

Purpose: Bacterial eye infections are frequently encountered in pediatric medical care, and empirical treatment may contribute to, and be complicated by, antibiotic resistance among causative pathogens. In vitro data from large, multi-center, multi-year surveillance studies are useful for tracking resistance to commonly used antibiotics. The Antibiotic Resistance Monitoring in Ocular Microorganisms (ARMOR) study, having completed its 10th year, is the only ongoing nationwide antibiotic resistance surveillance program specific to ocular bacteria. Here, …

Spatial Trends in Salmonella Infection in Pigs in Spain.

Salmonella is one of the most important foodborne pathogens worldwide. Its main reservoirs are poultry and pigs, in which infection is endemic in many countries. Spain has one of the largest pig populations in the world. Even though Salmonella infection is commonly detected in pig farms, its spatial distribution at the national level is poorly understood. Here we aimed to report the spatial distribution of Salmonella-positive pig farms in Spain and investigate the presence of potential spatial trends over a 17-year period. For this, data on samples from pigs tested for Salmonella in 2002–2013, 2015, 2017, and 2019 as part of the Spanish Veterinary Antimicrobial Resistance Surveillance program, representing 3,730 farms were analyzed. The spatial distribution and clustering of Salmonella-positive pig farms at the province level were explored using spatial empirical Bayesian smoothing and global Moran's I, local Moran's I, and the Poisson model of the spatial scan statistics. Bayesian spatial regression using a reparameterized Besag-York-Mollié Poisson model (BYM2 model) was then performed to quantify the presence of spatially structured and unstructured effects while accounting for the effect of potential risk factors for Salmonella infection at the province level. The overall proportion of Salmonella-positive farms was 37.8% (95% confidence interval: 36.2–39.4). Clusters of positive farms were detected in the East and Northeast of Spain. The Bayesian spatial regression revealed a West-to-East increase in the risk of Salmonella infection at the province level, with 65.2% (50% highest density interval: 70–100.0%) of this spatial pattern being explained by the spatially structured component. Our results demonstrate the existence of a spatial variation in the risk of Salmonella infection in pig farms at the province level in Spain. This information can help to optimize risk-based Salmonella surveillance programs in Spain, although further research to identify farm-level factors explaining this pattern are needed.

Inherent colistin resistance in genogroups of the Enterobacter cloacae complex: epidemiological, genetic and biochemical analysis from the BSAC Resistance Surveillance Programme.

Polymyxins have re-entered use against problem Gram-negative bacteria. Resistance rates are uncertain, with estimates confounded by selective testing. The BSAC Resistance Surveillance Programme has routinely tested colistin since 2010; we reviewed data up to 2017 for relevant Enterobacterales (n = 10 914). Unexpectedly frequent resistance was seen among the Enterobacter cloacae complex isolates (n = 1749); for these, we investigated relationships to species, genome, carbon source utilization and LPS structure. Annual colistin resistance rates among E. cloacae complex isolates were 4.4%-20%, with a rising trend among bloodstream organisms; in contrast, annual rates for Escherichia coli and Klebsiella spp. (including K. aerogenes) generally remained <2%. WGS split the E. cloacae complex isolates into seven genogroup clusters, designated A-G. Among isolates assigned to genogroups A-D, 47/50 sequenced were colistin resistant, and many of those belonging to genogroups A-C identified as E. asburiae. Isolates belonging to genogroups E-G consistently identified as E. cloacae and were rarely (only 3/45 representatives sequenced) colistin resistant. Genogroups F and G, the predominant colistin-susceptible clusters, were metabolically distinct from other clusters, notably regarding utilization or not of l-fucose, formic acid, d-serine, adonitol, myo-inositol, l-lyxose and polysorbates. LPS from resistant organisms grown without colistin pressure lacked substitutions with 4-amino-arabinose or ethanolamine but was more structurally complex, with more molecular species present. Colistin resistance is frequent in the E. cloacae complex and increasing among bloodstream isolates. It is associated with: (i) particular genomic and metabolic clusters; (ii) identification as E. asburiae; and (iii) with more complex LPS architectures.

Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, genomic surveillance is rare in low- and middle-income countries. Here, we implement WGS within the established Antimicrobial Resistance Surveillance Program of the Philippines via a binational collaboration. In parallel, we characterize bacterial populations of key bug-drug combinations via a retrospective sequencing survey. By linking the resistance phenotypes to genomic data, we reveal the interplay of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying the expansion of specific resistance phenotypes that coincide with the growing carbapenem resistance rates observed since 2010. Our results enhance our understanding of the drivers of carbapenem resistance in the Philippines, while also serving as the genetic background to contextualize ongoing local prospective surveillance.

Comparison of Microdilution Method with Agar Dilution Method for Antibiotic Susceptibility Test of Neisseria gonorrhoeae.

IntroductionAntimicrobial resistance (AMR) of Neisseria gonorrhoeae (N. gonorrhoeae) becomes a grave public health problem in the world. A strengthened Antimicrobial Resistance Surveillance Program is needed to track the trend of AMR development. However, the lack of a proper antimicrobial susceptibility test (AST) method is a barrier to expand the AMR surveillance in China. Traditional agar dilution (AD) method is laborious and E-test strips have no approval license for clinical use. Herein, a Chinese group modified the microdilution (MD) method for clinical ASTs. The objective of this study is to compare the MD method with the AD method for N. gonorrhoeae AST.Materials and MethodsA total of 166 clinical isolates were tested for antimicrobial susceptibility of ceftriaxone, spectinomycin, azithromycin, ciprofloxacin, tetracycline, and penicillin using MD and AD method simultaneously. Results of MD method were read manually or automatically. Rates of essential agreement (EA), category agreement (CA), minor error, and very major error were compared.ResultsThe total EAs (compared with results read manually) of penicillin, tetracycline, ciprofloxacin, spectinomycin, ceftriaxone, and azithromycin were 90.4%, 97.0%, 85.5%, 100.0%, 94%, and 72.3%; and CAs were 82.5%, 94.0%, 100%, 100%, 95.2%, and 94%, respectively.ConclusionWe conclude that the MD method might be an alternative for clinical AST of N. gonorrhoeae in China. In particular, MD method has the potency of accurate differentiation of isolates resistant to ceftriaxone or azithromycin, which were empirically recommended for gonococcal treatment, but its quality remained suboptimal, and further improvement is needed for clinical use.

Detection of multidrug-resistant Gram-negative bacteria from imported reptile and amphibian meats.

The food supply is a potential source of antimicrobial resistance. Current surveillance programmes targeting food are limited to beef, pork and poultry and do not capture niche products. In this study, imported reptile and amphibian products were screened for antimicrobial-resistant bacteria. In all, 53 items including soft shell turtles, frog legs, geckos, snakes and a turtle carapace were purchased from specialty markets in Vancouver and Saskatoon, Canada. Samples were selectively cultured for Salmonella sp., Escherichia coli, extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and meropenem-resistant organisms. Salmonella, all pan-susceptible, were grown from six dried geckos. Escherichia coli were isolated from 19 samples, including ESBL producers from six items. One multidrug-resistant E. coli possessed both the blaCTX-M-55 and mcr-1 genes. An NDM-1-producing Acinetobacter sp. was also isolated from a dried turtle carapace. Our results suggest that imported reptile and amphibian meats are an underappreciated source of resistant bacteria. The international trade of food may play a role in the dissemination of resistant bacteria. The presence of these bacteria in niche market foods represents a risk of unknown magnitude to public health and a gap in current national resistance surveillance programmes.

A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella Pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program.

Multidrug-resistant Klebsiella pneumoniae (MDR Kp), in particular carbapenem-resistant Kp (CR-Kp), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR-Kp (CRCR-Kp). During the period 2013–2014, 27 CRCR-Kp nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as blaKPC, related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes mcr 1–9 were not detected, while known and new genetic variations in mgrB, phoQ, and pmrB were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as IncFIB(pQil), IncFIB(K), ColRNAI, IncX3, and IncFII(K) types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR-Kp nosocomial strains and could help to limit their diffusion.

Population Genomics of Mycobacterium leprae Reveals a New Genotype in Madagascar and the Comoros.

Human settlement of Madagascar traces back to the beginning of the first millennium with the arrival of Austronesians from Southeast Asia, followed by migrations from Africa and the Middle East. Remains of these different cultural, genetic, and linguistic legacies are still present in Madagascar and other islands of the Indian Ocean. The close relationship between human migration and the introduction and spread of infectious diseases, a well-documented phenomenon, is particularly evident for the causative agent of leprosy, Mycobacterium leprae. In this study, we used whole-genome sequencing (WGS) and molecular dating to characterize the genetic background and retrace the origin of the M. leprae strains circulating in Madagascar (n = 30) and the Comoros (n = 3), two islands where leprosy is still considered a public health problem and monitored as part of a drug resistance surveillance program. Most M. leprae strains (97%) from Madagascar and Comoros belonged to a new genotype as part of branch 1, closely related to single nucleotide polymorphism (SNP) type 1D, named 1D-Malagasy. Other strains belonged to the genotype 1A (3%). We sequenced 39 strains from nine other countries, which, together with previously published genomes, amounted to 242 genomes that were used for molecular dating. Specific SNP markers for the new 1D-Malagasy genotype were used to screen samples from 11 countries and revealed this genotype to be restricted to Madagascar, with the sole exception being a strain from Malawi. The overall analysis thus ruled out a possible introduction of leprosy by the Austronesian settlers and suggests a later origin from East Africa, the Middle East, or South Asia.

A Sensitive and Cost-Effective Method for Isolation of Staphylococcus aureus from Agricultural Soils Suitable for Antimicrobial Resistance Surveillance Programs

A Sensitive and Cost-Effective Method for Isolation of Staphylococcus aureus from Agricultural Soils Suitable for Antimicrobial Resistance Surveillance Programs

Occurrence of Multidrug-resistant Uropathogens Implicated in Asymptomatic Bacteriuria in Adults with Sickle Cell Disease in Ile-Ife, Southwest Nigeria.

ObjectivesWe sought to determine the prevalence of asymptomatic bacteriuria (ASB) in patients with sickle cell disease (SCD), the susceptibility profile of its agents and their extended-spectrum β-lactamase (ESBL) production.MethodsFifty-nine patients with SCD and 116 healthy controls were investigated. Urine samples were collected and cultured by standard techniques. We used the disc diffusion technique to determine antibiotic susceptibility. ESBL was detected by the combination disc method and detection of blaSHV, blaTEM, and blaCTX-M genes by multiplex-polymerase chain reaction.ResultsThe prevalence of ASB was higher among patients with SCD (8.6%) than controls (0.9%) (p = 0.016), predominantly among females. Coagulase-negative staphylococci (n = 2; 33.3%) predominated among the isolates. Other uropathogens included Stenotrophomonas maltophilia, Acinetobacter baumannii, and Enterobacter cloacae. All isolates were sensitive to meropenem but were resistant to ceftazidime, ampicillin, and tetracycline. blaSHV, blaTEM, and blaCTX-M-15 were detected in Enterobacter cloacae.ConclusionsThe prevalence of ASB is high in patients with SCD predominantly among females. Rare multidrug-resistant uropathogens were implicated. We posit a need for resistance surveillance programs and antibiotic stewardship to prevent treatment failure and reduce drug resistance.

A Fifteen-Year Report of Serotype Distribution and Antimicrobial Resistance of Salmonella in the Philippines

Background. Salmonella enterica ser. Typhi and Salmonella enterica ser. Paratyphi are agents of typhoid fever, a severe systemic disease, which remains to be a public health concern in the Philippines. Infection due to non-typhoidal Salmonella (NTS), on the other hand, most often results in a self-limiting acute gastroenteritis but may result in invasive disease in some cases.&nbsp; There is scarcity of information on the Salmonella serotypes in the Philippines which limits understanding of the distribution, transmission and antimicrobial resistance of these bacteria. Objective. This study describes the serotype distribution and antimicrobial resistance of Salmonella in the Philippines over a 15-year period. Methodolgy. Salmonella isolates were collected through the Philippine Department of Health-Antimicrobial Resistance Surveillance Program (DOH-ARSP) from January 1, 2004 to December 31, 2018. The isolates were serotyped using Sven Gard method for slide agglutination using antigens from Denka Seiken (Japan), and S and A serotest (Thailand). Antigenic formula obtained were classified according to White-Kauffmann-LeMinor scheme. Antimicrobial susceptibility testing for ampicillin, ceftriaxone, cefotaxime, chloramphenicol, ciprofloxacin, and trimethoprim-sulfamethoxazole, were performed using both automated and conventional methods (Kirby Bauer disk diffusion and gradient diffusion method). Antimicrobial susceptibility results were interpreted using Clinical and Laboratory Standards Institute (CLSI) 2018 interpretive criteria (M100Ed28E). Results. A total of 2,387 isolates were collected from human specimens during the 15-year study period. There were 69 serotypes of Salmonella identified with the most common being Salmonella enterica ser. Typhi: n=1895 (79.39%), Salmonella enterica ser. Enteritidis: n=182 (7.62%), Salmonella enterica ser. Typhimurium: n=87 (3.64%), Salmonella enterica ser. &nbsp;Weltevreden: n=24 (1.00%), Salmonella enterica ser. Paratyphi A: n=17 (0.71%), Salmonella enterica ser. Stanley: n=17 (0.71%), Salmonella&nbsp; enterica ser. Anatum: n=13 (0.54%), Salmonella enterica ser. Heidelberg: n=12 (0.50%), Salmonella enterica ser. Choleraesuis var. Kunzendorf: n=9 (0.38%). The multidrug resistant Salmonella serotypes reported in this study were mostly resistant to ampicillin, cefotaxime, ciprofloxacin combinations. Conclusion. This present study showed that prevailing Salmonella serotypes in the Philippines were similar with Salmonella serotypes reported from other Asian countries. Typhoidal isolates were high among 6-17 years old and were mostly from males. The antimicrobial resistance rates for typhoidal Salmonella isolates to ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole, ciprofloxacin, ceftriaxone and cefotaxime were lower compared with the antimicrobial resistance rates for non-typhoidal Salmonella isolates. Multidrug resistance for both Salmonella Typhi and NTS were relatively low. Continued and enhanced surveillance is needed to monitor the rising levels of antimicrobial resistance, determine risk factors and exposures associated with Salmonella Typhi and NTS infection to guide prevention and control measures.

Progress towards a coordinated, national paediatric antimicrobial resistance surveillance programme: Staphylococcus aureus, enterococcal and Gram-negative bacteraemia in Australia.

There is increasing knowledge of antimicrobial usage in children yet limited availability of nationally representative paediatric-specific data on antimicrobial resistance. Paediatric data from this national surveillance programme are presented to explore differences between childhood and adult bloodstream infections and antimicrobial resistance surveillance. Using information collected from a prospective coordinated antimicrobial resistance surveillance programme, children ≤18 years and adults >18 years with a positive blood culture for Staphylococcus aureus, Enterococcus spp. or Gram-negative spp. presenting to one of 34 Australian hospitals during 2013-16 were evaluated. Consistent methodologies for key sepsis pathogens were employed and a comparative analysis between children and adults was conducted. There are stark contrasts between children and adults in this national antimicrobial resistance (AMR) data set. Notable differences include lower rates of AMR, different clinical and molecular phenotypes and lower mortality amongst children. The burden of Gram-negative resistance is disproportionately experienced in children, with higher odds of death with an ESBL versus non-ESBL bacteraemia in comparison with adults. These data support that children are not just 'little adults' in the AMR era, and analyses by age group are important to detect differences in antibiotic susceptibility, clinical phenotype and genetic virulence factors. Antimicrobial surveillance incorporated into routine laboratory practice is vital to inform an array of wider applications including antimicrobial guidelines, stewardship and direction for prioritization of novel antimicrobial development.

Resistance trends among Enterobacterales from bacteraemias in the UK and Ireland, 2007 - 2017

Background The British Society for Antimicrobial Chemotherapy (BSAC) Bacteraemia Resistance Surveillance Programme monitors the antimicrobial susceptibility of organisms causing bacteraemias in the UK and Ireland. We review data for Escherichia coli, Klebsiella, Enterobacter, Proteeae, and Serratia collected between 2007-2017. Methods Consecutive isolates causing clinically significant bacteraemia were tested; participating laboratories (n=24-40) collected 7-20 isolates/species per year. Minimum inhibitory concentrations were determined centrally by BSAC agar dilution. Results Rates of resistance in the UK and Ireland remained largely stable over the 11-year period, during which 14,206 isolates were tested [(E. coli, n=5364; Klebsiella, n=3016; Proteeae, n=2423; Enterobacter, n=1819, and Serratia, n=1584)]. A decrease in resistance to piperacillin/tazobactam was noted among all species, except K. aerogenes. A decrease in resistance to ciprofloxacin was seen among E. coli and Enterobacter. Average rates of resistance to ceftolozane/tazobactam ranged from 0.2% (E. coli)to 9.2%(E. cloacae), whereas rates of resistance to ceftobiprole were higher [10% (E. coli) and 20% (E. cloacae)]. Rates of colistin resistance were low among E. coli (0.5%), and Klebsiella (1.2%); however, rates were higher, and increasing among Enterobacter (6.1% in 2011 to 13.4% in 2017). Rates of ESBL production were stable over time; higher among E. coli (9.6%), Enterobacter (10.4%), and Klebsiella (14.7%), compared with &lt;1% among Proteeae and Serratia. Carbapenemase producers remained rare (n=16 over 11 years, without trend). Conclusion The largely unchanging or reducing resistance rates among Enterobacterales causing bacteraemia are reassuring and may reflect interventions to reduce inappropriate use of antimicrobials implemented across the countries surveyed.

Antimicrobial resistance of commensal Escherichia coli from food-producing animals in Russia.

Background and Aim:Commensal Escherichia coli is an important indicator of antimicrobial resistance (AMR) in animals and food of animal origin. Therefore, it was recommended by the World Health Organization and OIE for inclusion in resistance surveillance programs. At the same time, the data on E. coli isolates from animals in Russia are scarce. The aim of this work was to determine the current prevalence of resistance and genetic markers of non-pathogenic commensal E. coli collected from major food-producing animals (poultry, pigs, and cows) in different regions of Russia and to compare these data with data from other countries to prioritize antimicrobials for limiting their use according to the National Action PlanMaterials and Methods:Samples (n=306) were collected from biomaterial of chicken, turkey, cows, and pigs raised on 11 farms in the European part of Russia, Siberia, and North Caucasus. Isolates (n=306) of E. coli were tested for resistance to 11 antimicrobials from ten classes using the broth microdilution method. MICs were interpreted against EUCAST microbiological and clinical breakpoints. For data analysis and statistical processing, the AMRcloud online platform was used. The data are presented in comparison with other countries.Results:In Russia, higher levels of microbiological and clinical resistance of E. coli to critically important antimicrobials, including colistin, cefotaxime, and ciprofloxacin, were found compared to other countries, especially in poultry: About 30% of isolates from chicken were resistant to colistin, 8% to cefotaxime, and 88% to ciprofloxacin according to EUCAST ECOFFs. Only 10% of isolates from cows were resistant to cefotaxime. About 47% of isolates of E. coli from chicken had a moderate relative resistance for ampicillin and 56% for tetracycline. For most antimicrobials, isolates from cows demonstrated a lower resistance than isolates from poultry and pigs. All tested isolates from chicken, turkey, and pigs showed a simultaneous microbiological resistance to at least three classes of antimicrobials. No pan-resistant isolates were found.Conclusion:High levels of AMR of commensal E. coli from poultry, especially for critically important drugs, are a matter of concern and should be taken into account when choosing antimicrobials to be restricted for use in animal husbandry according to the National Action Plan.

A direct qPCR screening approach to improve the efficiency of Mycoplasma bovis isolation in the frame of a broad surveillance study

Culturing Mycoplasma bovis is laborious and unpredictable with most laboratories relying on molecular methods for its detection and identification. However, bacterial culture is still necessary to relate phenotypic characteristics to genotypic traits within and between individual strains. Thus, the main objective of this study was to develop a procedure that saved time and consumables during the culturing of M. bovis within the scope of a broad antimicrobial resistance surveillance project. Deep nasopharyngeal swabs (DNPS) collected from feedlot cattle upon arrival at 10 Southern Alberta feedlots were enriched in broth and an aliquot of the culture was directly used in a M. bovis-specific quantitative PCR (qPCR) assay. Only qPCR-positive cultures were plated onto agar media for the isolation of M. bovis. The detection of M. bovis from broth culture by direct-culture-qPCR proved to be more sensitive (1.61 × 102 CFU/mL) than using a commercial kit (1.61 × 103 CFU/mL) to extract DNA from pure cultures of M. bovis. When isolation of M. bovis from broth-enriched DNPS (n = 208 samples) was used as the gold standard for diagnostics, the qPCR screening approach showed 100% sensitivity, 87.27% specificity, and a kappa index = 0.87 (strong agreement). In contrast, qPCR of DNPS samples (n = 58) exhibited 100% sensitivity, 42.86% specificity, and a kappa index = 0.49 (weak agreement). The qPCR protocol described here together with a high throughput direct-culture-qPCR approach for sample testing made it possible to reduce the labor and cost of M. bovis isolation by eliminating the need to process 97.3% of M. bovis-negative samples. This was possible through the use of qPCR Ct values as a predictive tool of the likelihood of M. bovis isolation. This new procedure could be evaluated for its use in antimicrobial resistance surveillance programs that focus on Mycoplasma species.

Antibiotic resistance among ocular bacterial pathogens from pediatric patients

The Antibiotic Resistance Monitoring in Ocular micRoorganisms (ARMOR) study is a nationwide antibiotic resistance surveillance program specific to bacterial pathogens encountered in ocular infections. We report in vitro antimicrobial resistance data for isolates collected from pediatric patients from 2009 through 2017.

Molecular Characterization of HIV-1 Minority Subtypes in Hong Kong: A Recent Epidemic of CRF07_BC among the Men who have Sex with Men Population.

Over the past years, an increasing trend was noticed for non-B and non- CRF01_AE HIV-1 strains prevalence in Hong Kong. In this study, we aimed at using the available HIV-1 pol sequences collected from 1994 to 2013 through our local antiretroviral resistance surveillance program to investigate the molecular epidemiology and evolution of HIV-1 minority subtypes in Hong Kong. We also aimed at investigating their potential association and impact of those transmission risk groups. A total of 2,315 HIV-1 partial pol sequences were included. HIV-1 genotypes were determined by REGA Genotyping Tool and phylogenetic analysis with reference sequences. The viral evolutionary rates and time of the most common ancestor (tMRCA) were estimated by Bayesian Markov Chain Monte Carlo (MCMC) interference. Apart from the two prevalent HIV-1 genotypes in Hong Kong (subtype B,41.6%, CRF01_AE,40.5%), phylogenetic analysis revealed a broad viral diversity including CRF07_BC(5.1%), subtype C(4.5%), CRF02_AG(1.1%), CRF08_BC(0.8%), subtype A1(0.8%), subtype G(0.4%), subtype D(0.4%), CRF06_cpx(0.4%), subtype F(0.1%), CRF12_BF(0·04%) and other recombinants(4.5%). The top five minority subtypes were further analyzed which demonstrated distinct epidemiological and phylogenetic patterns. Over 70% of subtypes A1, C and CRF02_AG infections were circulated among non-Chinese Asians or African community in Hong Kong and were mainly transmitted between heterosexual regular partners. Instead, over 90% of CRF07_BC and CRF08_BC patients were Chinese. An epidemic cluster was identified in CRF07_BC and estimated to expand from 2002 onwards based on skyline plot and molecular clock analysis. Our results highlighted the emergence of CRF07_BC epidemic in local MSM community, public health interventions targeting the community should be further enhanced to tackle the epidemic.

Enhancing the one health initiative by using whole genome sequencing to monitor antimicrobial resistance of animal pathogens: Vet-LIRN collaborative project with veterinary diagnostic laboratories in United States and Canada

BackgroundAntimicrobial resistance (AMR) of bacterial pathogens is an emerging public health threat. This threat extends to pets as it also compromises our ability to treat their infections. Surveillance programs in the United States have traditionally focused on collecting data from food animals, foods, and people. The Veterinary Laboratory Investigation and Response Network (Vet-LIRN), a national network of 45 veterinary diagnostic laboratories, tested the antimicrobial susceptibility of clinically relevant bacterial isolates from animals, with companion animal species represented for the first time in a monitoring program. During 2017, we systematically collected and tested 1968 isolates. To identify genetic determinants associated with AMR and the potential genetic relatedness of animal and human strains, whole genome sequencing (WGS) was performed on 192 isolates: 69 Salmonella enterica (all animal sources), 63 Escherichia coli (dogs), and 60 Staphylococcus pseudintermedius (dogs).ResultsWe found that most Salmonella isolates (46/69, 67%) had no known resistance genes. Several isolates from both food and companion animals, however, showed genetic relatedness to isolates from humans. For pathogenic E. coli, no resistance genes were identified in 60% (38/63) of the isolates. Diverse resistance patterns were observed, and one of the isolates had predicted resistance to fluoroquinolones and cephalosporins, important antibiotics in human and veterinary medicine. For S. pseudintermedius, we observed a bimodal distribution of resistance genes, with some isolates having a diverse array of resistance mechanisms, including the mecA gene (19/60, 32%).ConclusionThe findings from this study highlight the critical importance of veterinary diagnostic laboratory data as part of any national antimicrobial resistance surveillance program. The finding of some highly resistant bacteria from companion animals, and the observation of isolates related to those isolated from humans demonstrates the public health significance of incorporating companion animal data into surveillance systems. Vet-LIRN will continue to build the infrastructure to collect the data necessary to perform surveillance of resistant bacteria as part of fulfilling its mission to advance human and animal health. A One Health approach to AMR surveillance programs is crucial and must include data from humans, animals, and environmental sources to be effective.

Potentiation of imipenem by relebactam for Pseudomonas aeruginosa from bacteraemia and respiratory infections.

Imipenem resistance in Pseudomonas aeruginosa most often entails loss of the 'carbapenem-specific' porin OprD; more rarely it reflects acquired carbapenemases. Loss of OprD only confers resistance to imipenem if AmpC β-lactamase is expressed, and we investigated whether this mechanism was overcome by relebactam, a developmental diazabicyclooctane β-lactamase inhibitor. Consecutive P. aeruginosa isolates causing bacteraemia or hospital-onset lower respiratory tract infections were collected between 2014 and 2016 under the aegis of the BSAC Resistance Surveillance Programme. Imipenem MICs were determined centrally by BSAC agar dilution, with relebactam at a fixed concentration (4 mg/L). For most imipenem-susceptible P. aeruginosa (726/759, 95.7%), the MICs of imipenem alone were 0.5-2 mg/L and were decreased 3- to 4-fold by addition of relebactam, as based on geometric means or modes. For most imipenem-resistant P. aeruginosa (82/92, 89%), imipenem MICs were 8-16 mg/L, and were reduced to 1-2 mg/L by relebactam. These patterns applied regardless of whether the isolates were susceptible to penicillins and cephalosporins or had phenotypes suggesting derepressed AmpC or up-regulated efflux. Imipenem MICs for five P. aeruginosa with MBLs remained high (≥16 mg/L) regardless of relebactam. Potentiation of imipenem by relebactam was almost universal, in accordance with the view that endogenous pseudomonal AmpC ordinarily protects against this carbapenem to a small degree. Imipenem MICs were reduced to the current breakpoint, or lower, except for MBL producers. Potentiation was not compromised by derepression of AmpC or up-regulation of efflux.

Antimicrobial Resistance Surveillance and New Drug Development.

Surveillance represents an important informational tool for planning actions to monitor emerging antimicrobial resistance. Antimicrobial resistance surveillance (ARS) programs may have many different designs and can be grouped in 2 major categories based on their main objectives: (1) public health ARS programs and (2) industry-sponsored/product-oriented ARS programs. In general, public health ARS programs predominantly focus on health care and infection control, whereas industry ARS programs focus on an investigational or recently approved molecule(s). We reviewed the main characteristics of industry ARS programs and how these programs contribute to new drug development. Industry ARS programs are generally performed to comply with requirements from regulatory agencies responsible for commercial approval of antimicrobial agents, such as the US Food and Drug Administration, European Medicines Agency, and others. In contrast to public health ARS programs, which typically collect health care and diverse clinical data, industry ARS programs frequently collect the pathogens and perform the testing in a central laboratory setting. Global ARS programs with centralized testing play an important role in new antibacterial and antifungal drug development by providing information on the emergence and dissemination of resistant organisms, clones, and resistance determinants. Organisms collected by large ARS programs are extremely valuable to evaluate the potential of new agents and to calibrate susceptibility tests once a drug is approved for clinical use. These programs also can provide early evaluations of spectrum of activity and postmarketing trends required by regulatory agencies, and the programs may help drug companies to select appropriate dosing regimens and the appropriate geographic regions in which to perform clinical trials. Furthermore, these surveillance programs provide useful information on the potency and spectrum of new antimicrobial agents against indications and organisms in which clinicians have little or no experience. In summary, large ARS programs, such as the SENTRY Antimicrobial Surveillance Program, contribute key data for new drug development.