A narrative review on current duodenoscope reprocessing techniques and novel developments.

Duodenoscopy-associated infections occur worldwide despite strict adherence to reprocessing standards. The exact scope of the problem remains unknown because a standardized sampling protocol and uniform sampling techniques are lacking. The currently available multi-society protocol for microbial culturing by the Centers for Disease Control and Prevention, the United States Food and Drug Administration (FDA) and the American Society for Microbiology, published in 2018 is too laborious for broad clinical implementation. A more practical sampling protocol would result in increased accessibility and widespread implementation. This will aid to reduce the prevalence of duodenoscope contamination. To reduce the risk of duodenoscopy-associated pathogen transmission the FDA advised four supplemental reprocessing measures. These measures include double high-level disinfection, microbiological culturing and quarantine, ethylene oxide gas sterilization and liquid chemical sterilization. When the supplemental measures were advised in 2015 data evaluating their efficacy were sparse. Over the past five years data regarding the supplemental measures have become available that place the efficacy of the supplemental measures into context. As expected the advised supplemental measures have resulted in increased costs and reprocessing time. Unfortunately, it has also become clear that the efficacy of the supplemental measures falls short and that duodenoscope contamination remains a problem. There is a lot of research into new reprocessing methods and technical applications trying to solve the problem of duodenoscope contamination. Several promising developments such as single-use duodenoscopes, electrolyzed acidic water, and vaporized hydrogen peroxide plasma are already applied in a clinical setting.

Effects of antibiotic resistance, drug target attainment, bacterial pathogenicity and virulence, and antibiotic access and affordability on outcomes in neonatal sepsis: an international microbiology and drug evaluation prospective substudy (BARNARDS).

BACKGROUND: Sepsis is a major contributor to neonatal mortality, particularly in low-income and middle-income countries (LMICs). WHO advocates ampicillin-gentamicin as first-line therapy for the management of neonatal sepsis. In the BARNARDS observational cohort study of neonatal sepsis and antimicrobial resistance in LMICs, common sepsis pathogens were characterised via whole genome sequencing (WGS) and antimicrobial resistance profiles. In this substudy of BARNARDS, we aimed to assess the use and efficacy of empirical antibiotic therapies commonly used in LMICs for neonatal sepsis. METHODS: In BARNARDS, consenting mother-neonates aged 0-60 days dyads were enrolled on delivery or neonatal presentation with suspected sepsis at 12 BARNARDS clinical sites in Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Stillborn babies were excluded from the study. Blood samples were collected from neonates presenting with clinical signs of sepsis, and WGS and minimum inhibitory concentrations for antibiotic treatment were determined for bacterial isolates from culture-confirmed sepsis. Neonatal outcome data were collected following enrolment until 60 days of life. Antibiotic usage and neonatal outcome data were assessed. Survival analyses were adjusted to take into account potential clinical confounding variables related to the birth and pathogen. Additionally, resistance profiles, pharmacokinetic-pharmacodynamic probability of target attainment, and frequency of resistance (ie, resistance defined by in-vitro growth of isolates when challenged by antibiotics) were assessed. Questionnaires on health structures and antibiotic costs evaluated accessibility and affordability. FINDINGS: Between Nov 12, 2015, and Feb 1, 2018, 36 285 neonates were enrolled into the main BARNARDS study, of whom 9874 had clinically diagnosed sepsis and 5749 had available antibiotic data. The four most commonly prescribed antibiotic combinations given to 4451 neonates (77·42%) of 5749 were ampicillin-gentamicin, ceftazidime-amikacin, piperacillin-tazobactam-amikacin, and amoxicillin clavulanate-amikacin. This dataset assessed 476 prescriptions for 442 neonates treated with one of these antibiotic combinations with WGS data (all BARNARDS countries were represented in this subset except India). Multiple pathogens were isolated, totalling 457 isolates. Reported mortality was lower for neonates treated with ceftazidime-amikacin than for neonates treated with ampicillin-gentamicin (hazard ratio [adjusted for clinical variables considered potential confounders to outcomes] 0·32, 95% CI 0·14-0·72; p=0·0060). Of 390 Gram-negative isolates, 379 (97·2%) were resistant to ampicillin and 274 (70·3%) were resistant to gentamicin. Susceptibility of Gram-negative isolates to at least one antibiotic in a treatment combination was noted in 111 (28·5%) to ampicillin-gentamicin; 286 (73·3%) to amoxicillin clavulanate-amikacin; 301 (77·2%) to ceftazidime-amikacin; and 312 (80·0%) to piperacillin-tazobactam-amikacin. A probability of target attainment of 80% or more was noted in 26 neonates (33·7% [SD 0·59]) of 78 with ampicillin-gentamicin; 15 (68·0% [3·84]) of 27 with amoxicillin clavulanate-amikacin; 93 (92·7% [0·24]) of 109 with ceftazidime-amikacin; and 70 (85·3% [0·47]) of 76 with piperacillin-tazobactam-amikacin. However, antibiotic and country effects could not be distinguished. Frequency of resistance was recorded most frequently with fosfomycin (in 78 isolates [68·4%] of 114), followed by colistin (55 isolates [57·3%] of 96), and gentamicin (62 isolates [53·0%] of 117). Sites in six of the seven countries (excluding South Africa) stated that the cost of antibiotics would influence treatment of neonatal sepsis. INTERPRETATION: Our data raise questions about the empirical use of combined ampicillin-gentamicin for neonatal sepsis in LMICs because of its high resistance and high rates of frequency of resistance and low probability of target attainment. Accessibility and affordability need to be considered when advocating antibiotic treatments with variance in economic health structures across LMICs. FUNDING: The Bill & Melinda Gates Foundation.

Use of Monte Carlo simulation to optimize antibiotic selection for bloodstream infections caused by Enterobacteriaceae in Shandong Province, China.

The increasing rates of resistance to ß-lactams have made it more challenging for clinicians to select appropriate antibiotic treatment for bloodstream infections (BSIs) caused by suspected Enterobacteriaceae. The objective of this analysis was to determine the optimal dosage regimens of ß-lactams for treatment of BSIs based on analysis of 19,334 Enterobacteriaceae collected from blood specimens. Monte Carlo simulation using pharmacokinetic parameters of infected patients was performed to determine the probability of overall pharmacokinetic/pharmacodynamic (PK/PD) target attainment (OPTA). E. coli, K. pneumoniae, and E. cloacae were the 3 most common species. Nine of the 16 tested regimens had optimal OPTAs (>90%) for Enterobacteriaceae overall (meropenem 2g q8h, 3 h infusion; meropenem 2g q8h, 0.5h; meropenem 1g q8h, 0.5h; piperacillin/tazobactam 4.5g q8h, 3h; ceftazidime 2g q8h, 3h; imipenem 0.5g q6h, 0.5h; imipenem 1g q8h, 0.5h; piperacillin/tazobactam 3.375g q6h, 0.5h; ceftazidime 2g q8h, 0.5h). Four other regimens had sub-optimal OPTAs of 80 to 90% (piperacillin/tazobactam 4.5g q8h, 0.5h; ceftazidime 1g q8h, 0.5h; cefepime 2g q12h, 3h; and cefepime 2g q12h, 0.5h). Although there are high antibiotic MICs among Enterobacteriaceae in Shandong Province, carbapenem- , ceftazidime- and piperacillin/tazobactam- based regimens provide the optimal treatment.

Prevalence, etiology, and economic impact of clinical mastitis on large dairy farms in China.

This study investigated the continuous monthly prevalence of bovine clinical mastitis (CM) and the distribution of causative pathogens among 36,619 CM milk samples from large dairy farms across seven Chinese provinces from 2015 to 2017 using data from routine CM recording systems. Based on treatment period and cost per cow, withdrawal period, daily milk production, and milk value data from each farm in 2017, we calculated the economic impact of CM at the farm level with 2578-9044 lactating cows per farm. Results showed a wide variation in monthly prevalence of CM (0.6 %-18.2 %) among the seven farms over the study period, indicating regional and temporal differences in the occurrence of CM in China. Enterobacteriaceae were the predominant pathogens across all farms from six provinces except Shandong, in which the Streptococcus spp. was the most prevalent. However, the distribution of various Enterobacteriaceae species differed among farms, and Streptococcus species distribution was strongly associated (Pearson's coefficient, 68.4 %) with location. Monthly economic losses associated with CM showed clear variation, ranging from 12,000-76,000 USD/farm/month. Sensitivity analysis showed that economic loss at the farm level was most sensitive to variation in the prevalence of CM, followed by antibiotic treatment period and daily milk production per cow. To our knowledge, this is the longest running study of CM and the first estimation of its economic impacts in China. Our findings highlight the considerable costs associated with mastitis, and indicate that preventive measures and regional and timely treatment of CM are needed.

Fight Against Antimicrobial Resistance: We Always Need New Antibacterials but for Right Bacteria.

Antimicrobial resistance in bacteria is frightening, especially resistance in Gram-negative Bacteria (GNB). In 2017, the World Health Organization (WHO) published a list of 12 bacteria that represent a threat to human health, and among these, a majority of GNB. Antibiotic resistance is a complex and relatively old phenomenon that is the consequence of several factors. The first factor is the vertiginous drop in research and development of new antibacterials. In fact, many companies simply stop this R&D activity. The finding is simple: there are enough antibiotics to treat the different types of infection that clinicians face. The second factor is the appearance and spread of resistant or even multidrug-resistant bacteria. For a long time, this situation remained rather confidential, almost anecdotal. It was not until the end of the 1980s that awareness emerged. It was the time of Vancomycin-Resistance Enterococci (VRE), and the threat of Vancomycin-Resistant MRSA (Methicillin-Resistant Staphylococcus aureus). After this, there has been renewed interest but only in anti-Gram positive antibacterials. Today, the threat is GNB, and we have no new molecules with innovative mechanism of action to fight effectively against these bugs. However, the war against antimicrobial resistance is not lost. We must continue the fight, which requires a better knowledge of the mechanisms of action of anti-infectious agents and concomitantly the mechanisms of resistance of infectious agents.

The 3-day rule for stool cultures: should all patients with haematological malignancies be excluded?

OBJECTIVES: The '3-day rule' for stool culture ordering suggests that only selected inpatients with nosocomial diarrhoea should have stool cultures for enteropathogenic bacteria (EPBs). Patients with haematological malignancies are not included in this group. We have analysed the ordering of stool cultures at Laikon Hospital to investigate whether all patients with haematological malignancies should be excluded from the 3-day rule. METHODS: We have retrospectively analysed all inpatient stool specimens sent to the microbiology laboratory for enteropathogenic bacteria culture at Laikon Hospital, Athens, Greece, between January 1, 2014 and December 31, 2014. We classified stool cultures sent after the third day as 'appropriate', 'excluded' with standard rule, 'excluded' with haematological malignancies, and 'inappropriate'. RESULTS: During the study period, 1101/1593 inpatient stool cultures (69.1%) had been ordered after the third day of hospitalization. The total yield for inpatient EPB stool cultures was 0.7% (11/1593). The yield for 'appropriate' cultures was significantly higher than the yield of all 'excluded' specimens (3.7% (3/81) versus 0.3% (2/585), p 0.018) and to 'inappropriate' orders (3.7% (3/81) versus 0.0% (0/485), p 0.0028). There was no difference in the yield between specimens 'excluded' with the standard rule and 'excluded' with haematological malignancies. CONCLUSIONS: In our hospital, the yield of stool cultures from patients with haematological malignancies is similar to that of patients 'excluded' from the standard 3-day rule. If patients with haematological malignancies were not excluded from the rule, we would reduce the inpatient stool cultures by 13.6% (217/1593) at the cost of missing one positive stool culture.

The infection risk scan (IRIS): standardization and transparency in infection control and antimicrobial use.

Background: Infection control needs user-friendly standardized instruments to measure the compliance to guidelines and to implement targeted improvement actions. This abstract describes a tool to measure the quality of infection control and antimicrobial use, the Infection Risk Scan (IRIS). It has been applied in a hospital, several nursing homes and a rehabilitation clinic in the Netherlands. Method: The IRIS consists of a set of objective reproducible measurements, combining patient- and healthcare related variables, such as: hand hygiene compliance, environmental contamination using ATP measurements, prevalence of resistant microorganisms by active screening, availability of infection control preconditions, personal hygiene of healthcare workers, appropriate use of indwelling medical devices and appropriate use of antimicrobials. Results are visualized in a spider plot using traffic light colors to facilitate the interpretation. Results: The IRIS provided ward specific results within the hospital that were the basis for targeted improvement programs resulting in measurable improvements. Hand hygiene compliance increased from 43% to 66% (more than 1000 observations per IRIS, p < 0.000) and ATP levels were significantly reduced (p < 0.000). In the nursing homes, large differences were observed with environmental contamination as common denominator. Most remarkable were the difference in Extended Spectrum Beta-Lactamase Enterobacteriaceae (ESBL-E) prevalence (mean 11%, range 0-21%). Conclusion: The bundle approach and visualization of the IRIS makes it a useful infection prevention tool providing standardization and transparency. Targeted interventions can be started based on the results of the improvement plot and repeated IRIS can show the effect of interventions. In that way, a quality control cycle with continuous improvement can be achieved.

Assessment of in vivo efficacy of eravacycline against Enterobacteriaceae exhibiting various resistance mechanisms: a dose-ranging study and pharmacokinetic/pharmacodynamic analysis.

After the pharmacokinetic (PK) profile of eravacycline, a novel fluorocycline, was defined, understanding its pharmacodynamic (PD) profile became essential. This study aimed to assess the correlation of the PK/PD index fAUC/MIC (ratio of area under the free drug concentration-time curve to MIC) and its magnitude with eravacycline's efficacy against Enterobacteriaceae using an immunocompetent murine thigh infection model to resemble the immunocompetent environment in eravacycline's clinical trials. Eight Enterobacteriaceae isolates with various resistance mechanisms were tested. Eravacycline doses ranged from 1-10 mg/kg/day and were given either once daily (q24h) or divided into doses every 12 h (q12h) over the 24-h treatment period. Antibacterial efficacy was measured as the change in log10CFU at 24 h compared with 0 h controls. Composite data were modelled using a sigmoid Emax model. Eravacycline MICs ranged from 0.125-0.5 µg/mL. The mean fAUC/MIC magnitudes required for stasis and 1-log reduction for the eight isolates were 2.9 ± 3.1 and 5.6 ± 5.0, respectively. Whilst the humanised eravacycline regimen (2.5 mg/kg q12h) pharmacokinetically achieves an fAUC0-24 that is higher than the fAUC0-24 achieved with the 5 mg/kg q24h dose, the latter was associated with greater efficacy, raising a suggestive correlation of the peak free drug concentration to MIC (fCmax/MIC) ratio with eravacycline's efficacy. This study showed that the magnitudes associated with eravacycline's efficacy in an immunocompetent murine thigh model appear to be close to achievable targets in human. These data support further development of eravacycline for treatment of infections caused by drug-resistant Enterobacteriaceae.

Impact of Culture-Independent Diagnostic Testing on Recovery of Enteric Bacterial Infections.

Background: Culture-independent diagnostic tests (CIDTs) are increasingly used to identify enteric pathogens. However, foodborne illness surveillance systems have relied upon culture confirmation to estimate disease burden and identify outbreaks through molecular subtyping. This study examined the impacts of CIDT and estimated costs for culture verification of Shigella, Salmonella, Shiga toxin-producing Escherichia coli (STEC), and Campylobacter at the Tennessee Department of Health Public Health Laboratory (PHL). Methods: This observational study included laboratory and epidemiological surveillance data collected between years 2013-2016 from patients with the reported enteric illness. We calculated pathogen recovery at PHL based on initial diagnostic test type reported at the clinical laboratory. Adjusted prevalence ratios (PRs) and 95% confidence intervals (CIs) were estimated with modified Poisson regression. Estimates of cost were calculated for pathogen recovery from CIDT-positive specimens compared to recovery from culture-derived isolates. Results: During the study period, PHL received 5553 specimens from clinical laboratories from patients with the enteric illness. Pathogen recovery was 57% (984/1713) from referred CIDT-positive stool specimens and 95% (3662/3840) from culture-derived isolates (PR, 0.61 [95% CI, .56-.66]). Pathogen recovery from CIDT-positive specimens varied based on pathogen type: Salmonella (72%), Shigella (64%), STEC (57%), and Campylobacter (26%). Compared to stool culture-derived isolates, the cost to recover pathogens from 100 CIDT-positive specimens was higher for Shigella (US $6192), Salmonella (US $18373), and STEC (US $27783). Conclusions: Pathogen recovery was low from CIDT-positive specimens for enteric bacteria. This has important implications for the current enteric disease surveillance system, outbreak detection, and costs for public health programs.

Assessment of antimicrobial resistance transfer between lactic acid bacteria and potential foodborne pathogens using in vitro methods and mating in a food matrix.

The transferability of antimicrobial resistance from lactic acid bacteria (LAB) to potential pathogenic strains was studied using in vitro methods and mating in a food matrix. Five LAB donors containing either erythromycin or tetracycline resistance markers on transferable elements were conjugally mated with LAB (Enterococcus faecalis, Lactococcus lactis) and pathogenic strains (Listeria spp., Salmonella ssp., Staphylococcus aureus, and Escherichia coli). In vitro transfer experiments were carried out with the donors and recipients using both the filter and plate mating methods. The food matrix consisted of fermented whole milk (fermented with the LAB donors) with the pathogenic recipients added as contaminants during the production process. All transconjugants were confirmed by phenotypic and molecular methods. Erythromycin resistance transfer from LAB strains to Listeria spp. was observed using both in vitro mating methods at high transfer frequencies of up to 5.1 x 10(-4) transconjugants per recipient. Also, high frequency transfer (ranging from 2.7 x 10(-8) up to 1.1 x 10(-3) transconjugants per recipient) of both erythromycin and tetracycline-resistance was observed between LAB species using in vitro methods. No resistance transfer was observed to Salmonella spp., Staphylococcus aureus, and E. coli. The only conjugal transfer observed in the fermented milk matrix was for tetracycline resistance between two LAB strains (at a transfer frequency of 2.6 x 10(-7) transconjugants per recipients). This study demonstrates the transfer of antimicrobial resistance from LAB to Listeria spp. using in vitro methods and also the transfer of resistance between LAB species in a food matrix. It highlights the involvement of LAB as a potential source of resistance determinants that may be disseminated between LAB and pathogenic strains including Listeria spp. Furthermore, it indicates that food matrices such as fermented milks may provide a suitable environment to support gene exchange.

Scope of potential bacterial agents of diarrhoea and microbial assessment of quality of river water sources in rural Venda communities in South Africa.

The microbial quality of several, usually untreated, surface domestic water sources, used by rural communities in the Venda Region of South Africa, was assessed to gauge their fitness for human consumption and to highlight the possible impact of waterborne diseases. The water sources studied were six points on the Levubu River and the rivers Mutale, Ngwedi, Tshinane, Makonde, Mutshindudi and Mudaswali. Total and faecal coliform, heterotrophic bacteria, enterococci and coliphage counts were used as indicators/surrogates to estimate the degree of bacterial and viral contamination respectively by standard methods. The presence of potential bacterial agents of diarrhoea such as Salmonella, Shigella, Campylobacter, Plesiomonas, Aeromonas and Vibrio was also determined. Results showed that the ranges of counts with regard to all the water sources investigated were 2.9 x 10(2) - 6.3 x 10(4) CFU/100 mL for faecal coliforms, 6.0 x 10(2) - 3.7 x 10(4) CFU/100 mL for total coliforms, 1.8 x 10(2) - 1.3 x 10(6) CFU/mL for heterotrophic plate count, 1.0 x 10(1) - 3.7 x 10(4) CFU/100 mL for enterococci and 0-13 PFU/100 mL for coliphages. These values are far higher than the acceptable maximum limits prescribed for South Africa by the Dept of Water & Forestry and the Water Research Commission - 0 CFU/100 mL, 5 CFU/100 mL, 1.0 x 10(2) CFU/mL, 0 CFU/100 mL and 1 PFU/100 mL for faecal coliforms, total coliforms, heterotrophic bacteria, enterococci and coliphages respectively. Salmonella, Shigella, Vibrio cholerae, Campylobacter, Aeromonas and Plesiomonas were isolated from several of the water sources investigated. The use of these water sources for drinking and domestic purposes poses a serious threat to the health and well being of the users and calls for urgent government intervention.

Cost-effective techniques to control human enteropathogens on fresh poultry.

Salmonella is a multi-faceted problem that must be attacked on many fronts. The results of Food Safety and Inspection Service's Puerto Rico Bacterial Control Project confirmed that there is no "silver bullet." The project showed that a combination of management commitment, process control, and specific interventions at key control points can bring about significant improvements in the bacterial quality of fresh poultry.