Antimicrobial susceptibility among Gram-positive and Gram-negative organisms collected from the Latin American region between 2004 and 2015 as part of the Tigecycline Evaluation and Surveillance Trial

The burden of antimicrobial resistance in the Americas in 2019: a cross-country systematic analysis

Background

Antimicrobial resistance (AMR) is an urgent global health challenge and a critical threat to modern health care. Quantifying its burden in the WHO Region of the Americas has been elusive-despite the region's long history of resistance surveillance. This study provides comprehensive estimates of AMR burden in the Americas to assess this growing health threat.

Methods

We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with AMR for 23 bacterial pathogens and 88 pathogen-drug combinations for countries in the WHO Region of the Americas in 2019. We obtained data from mortality registries, surveillance systems, hospital systems, systematic literature reviews, and other sources, and applied predictive statistical modelling to produce estimates of AMR burden for all countries in the Americas. Five broad components were the backbone of our approach: the number of deaths where infection had a role, the proportion of infectious deaths attributable to a given infectious syndrome, the proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of pathogens resistant to an antibiotic class, and the excess risk of mortality (or duration of an infection) associated with this resistance. We then used these components to estimate the disease burden by applying two counterfactual scenarios: deaths attributable to AMR (compared to an alternative scenario where resistant infections are replaced with susceptible ones), and deaths associated with AMR (compared to an alternative scenario where resistant infections would not occur at all). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity.

Findings

We estimated 569,000 deaths (95% UI 406,000-771,000) associated with bacterial AMR and 141,000 deaths (99,900-196,000) attributable to bacterial AMR among the 35 countries in the WHO Region of the Americas in 2019. Lower respiratory and thorax infections, as a syndrome, were responsible for the largest fatal burden of AMR in the region, with 189,000 deaths (149,000-241,000) associated with resistance, followed by bloodstream infections (169,000 deaths [94,200-278,000]) and peritoneal/intra-abdominal infections (118,000 deaths [78,600-168,000]). The six leading pathogens (by order of number of deaths associated with resistance) were Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Together, these pathogens were responsible for 452,000 deaths (326,000-608,000) associated with AMR. Methicillin-resistant S. aureus predominated as the leading pathogen-drug combination in 34 countries for deaths attributable to AMR, while aminopenicillin-resistant E. coli was the leading pathogen-drug combination in 15 countries for deaths associated with AMR.

Interpretation

Given the burden across different countries, infectious syndromes, and pathogen-drug combinations, AMR represents a substantial health threat in the Americas. Countries with low access to antibiotics and basic health-care services often face the largest age-standardised mortality rates associated with and attributable to AMR in the region, implicating specific policy interventions. Evidence from this study can guide mitigation efforts that are tailored to the needs of each country in the region while informing decisions regarding funding and resource allocation. Multisectoral and joint cooperative efforts among countries will be a key to success in tackling AMR in the Americas.

Funding

Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.

Tigecycline Resistance-Associated Mutations in the MepA Efflux Pump in Staphylococcus aureus

Tigecycline is an important antibacterial drug for treating infection by clinical multidrug-resistant bacteria, and tigecycline-resistant Staphylococcus aureus (TRSA) has been increasingly reported in recent years. Notably, only rpsJ and mepA are associated with the tigecycline resistance of S. aureus. The mepA gene encodes MepA efflux pumps, and the overexpression of mepA has been confirmed to be directly related to tigecycline resistance. Although the mutations of MepA widely occur, the associations between TRSA and mutations of MepA are still unclear. In this study, we explored mutations in the mepA genes from various sources. Then, tigecycline resistance-associated mutations T29I, E287G, and T29I+E287G in MepA were identified, and their effects were evaluated through mutant deletion and complementation, tigecycline accumulation assay, and molecular docking experiments. Results showed that the MICs of tigecycline, gentamicin, and amikacin increased in special complementary transformants and recovered after the addition of the efflux pump inhibitor carbonyl cyanide 3-chlorophenylhydrazone (CCCP). The tigecycline accumulation assay of the mepA-deleted mutant strain and its complementary transformants showed that T29I, E287G, and T29I+E287G mutations promoted tigecycline efflux, and molecular docking showed that mutations T29I, E287G, and T29I+E287G decreased the binding energy and contributed to ligand binding. Moreover, we inferred the evolutionary trajectory of S. aureus under the selective pressure of tigecycline in vitro. Overall, our study indicated that mutations in MepA play important roles in tigecycline resistance in S. aureus. IMPORTANCE Previous analysis has shown that overexpression of MepA is an exact mechanism involved in tigecycline resistance apart from the rpsJ mutation and is usually dependent on the mutant mepR. However, no research has evaluated the effects of diverse mutations discovered in TRSA in MepA. This study demonstrates that the mutations in MepA confer resistance to tigecycline without overexpression and provides genotypic references for identifying TRSA. Although tigecycline resistance-associated mutations in MepA identified in this study have not been observed in clinical isolates, the mechanism should be explored given that S. aureus strains are prevalent in the environment. Measures should be implemented to contain TRSA within the time window before tigecycline resistance-associated mutations in MepA are prevalent.

Antibacterial Effect of 16 Essential Oils and Modulation of mex Efflux Pumps Gene Expression on Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates: Is Cinnamon a Good Fighter?

The purpose of the study was to describe the antimicrobial activity of 16 common essential oils (EOs) on multidrug-resistant (MDR) Pseudomonas aeruginosa clinical isolates, including the determination of the effects on mex efflux pumps gene expression. Seventy-two clinical isolates of P. aeruginosa collected between 2020-2022 were screened for susceptibility to EOs using Kirby-Bauer disk diffusion to identify potential candidates for future alternative therapies. The minimal inhibitory concentration (MIC) was further determined for the EO that proved antibacterial activity following the disk diffusion screening. Positive and negative controls were also used for method validation. Since cinnamon EO exhibited the best antimicrobial activity, it was further used to evaluate its influence on mex A, B, C, E, and X efflux pumps gene expression using real-time RT-PCR. Cinnamon EO inhibited all P. aeruginosa strains, followed by thyme EO (37.5%, n = 27) and lavender EO (12.5%, n = 9). The other EOs were less efficient. The MIC detection showed that cinnamon at a concentration of 0.05% v/v inhibited all MDR P. aeruginosa isolates. Thyme, turmeric, peppermint, basil, clove, and lavender EOs presented various results, most of them having activity at concentrations higher than 12.5% v/v. By studying the activity of cinnamon EO on mex efflux pumps, it was found that mexA and mexB (66.5%) were generally under-expressed. The remarkable results produced using the very low concentrations of cinnamon EO, with 100% antimicrobial activity against multi-, extended-, and pan- drug-resistant (MDR, XDR, PDR) P. aeruginosa clinical isolates, completed with the severe alteration of the RNA messaging system, supports its potential to be used as adjuvant treatment, with impact on therapeutic results.

Epidemiology and risk factors for mortality among methicillin-resistant Staphylococcus aureus bacteremic patients in Southern Brazil

This study aimed to evaluate the epidemiology and 30-day mortality of adult patients with methicillin-resistant Staphylococcus aureus (MRSA) bacteremia. We retrospectively reviewed the demographic and clinical data of adult patients with S. aureus bloodstream infections (BSI), admitted to a tertiary public teaching medical center in Porto Alegre, Southern Brazil, from January 2014 to December 2019. A total of 928 patients with S. aureus BSI were identified in the study period (68.5 per 100,000 patient-years), and the proportion of MRSA isolates was 22% (19-27%). Thus, 199 patients were included in the analyses. The median age was 62 (IQR: 51-74) years, Charlson Comorbidity Index (CCI) median was 5 (IQR: 3-6), the Pitt bacteremia score (PBS) median was 1 (IQR: 1-4), and the most common site of infection was skin and soft tissue (26%). Most infections were hospital-acquired (54%), empirical anti-MRSA treatment was initiated in 34% of the cases, and in 44% vancomycin minimum inhibitory concentration was 1.5mg/L or above. Sixty-two (31.2%) patients died up to 30 days after the bacteremia episode. Patients with more comorbid conditions (higher CCI; aOR 1.222, p = 0.006) and a more severe presentation (higher PBS; aOR 1.726, p<0.001) were independently associated with mortality. Empiric antimicrobial therapy with an anti-MRSA regimen was associated with reduced mortality (aOR 0.319, p = 0.016). Our study identified significant risk factors for 30-day mortality in patients with MRSA BSI in a population with a high incidence of S. aureus bacteremia. Empiric treatment with an anti-MRSA drug was a protective factor. No significant variation in the incidence of S. aureus BSI was recorded throughout the period.

Global update on the in vitro activity of tigecycline and comparators against isolates of Acinetobacter baumannii and rates of resistant phenotypes (2016-2018)

OBJECTIVES

This study presents 2016-2018 in vitro antimicrobial activity data and rates of resistant phenotypes for clinical isolates of Acinetobacter baumannii from Africa/Middle East, Asia/South Pacific, Europe, Latin America, and North America.

METHODS

A total of 4320 A. baumannii isolates were collected across all regions between 2016 and 2018. The in vitro antimicrobial activities of amikacin, colistin, levofloxacin, meropenem, and tigecycline were determined using the broth microdilution methodology of the Clinical and Laboratory Standards Institute. MICs were interpreted using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (version 11.0). Rates of subsets that were resistant to amikacin, colistin, levofloxacin, and meropenem, according to EUCAST breakpoints, are also presented.

RESULTS

In each region, tigecycline and colistin were active against isolates of A. baumannii (MIC₉₀ values, 1 or 2 mg/L) and the lowest rate of resistance was to colistin (1.2%-7.3%). The rates of resistance to the panel of agents were generally lower among A. baumannii from North America (1.3%-42.7%), compared with the other regions. Fewer than 11% of meropenem-resistant A. baumannii were also resistant to colistin. The rates of amikacin-, levofloxacin- and meropenem-resistant A. baumannii were lowest in North America and mostly higher in Africa/Middle East and Latin America.

CONCLUSION

In each geographical region, tigecycline and colistin maintained good in vitro antimicrobial activity against isolates of A. baumannii, including antimicrobial-resistant subsets. The higher rates of meropenem-resistant isolates, particularly in Africa/Middle East and Latin America, require continued monitoring because of the scarcity of effective treatment options.

Characterization of 67 Confirmed Clustered Regularly Interspaced Short Palindromic Repeats Loci in 52 Strains of Staphylococci

Staphylococcus aureus (S. aureus), which is one of the most important species of Staphylococci, poses a great threat to public health. Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune platform to combat foreign mobile genetic elements (MGEs) such as plasmids and phages. The aim of this study is to describe the distribution and structure of CRISPR-Cas system in S. aureus, and to explore the relationship between CRISPR and horizontal gene transfer (HGT). Here, we analyzed 67 confirmed CRISPR loci and 15 companion Cas proteins in 52 strains of Staphylococci with bioinformatics methods. Comparing with the orphan CRISPR loci in Staphylococci, the strains harboring complete CRISPR-Cas systems contained multiple CRISPR loci, direct repeat sequences (DR) forming stable RNA secondary structures with lower minimum free energy (MFE), and variable spacers with detectable protospacers. In S. aureus, unlike the orphan CRISPRs away from Staphylococcal cassette chromosome mec (SCCmec), the complete CRISPR-Cas systems were in J1 region of SCCmec. In addition, we found a conserved motif 5'-TTCTCGT-3' that may protect their downstream sequences from DNA interference. In general, orphan CRISPR locus in S. aureus differed greatly from the structural characteristics of the CRISPR-Cas system. Collectively, our results provided new insight into the diversity and characterization of the CRISPR-Cas system in S. aureus.

Prevalence of MDR bacteria in an acute trauma hospital in Port-au-Prince, Haiti: a retrospective analysis from 2012 to 2018

Background

Antibiotic resistance (ABR) is recognized as an increasing threat to global health. Haiti declared ABR an emerging public health threat in 2018, however, the current surveillance system is limited. We described the microbiological data from a Médecins Sans Frontières trauma hospital, to increase knowledge on ABR in Haiti for similar facilities.

Methods

A retrospective cross-sectional analysis of routine microbiological data of samples taken from patients admitted to the inpatient ward or followed up in the outpatient clinic of the trauma hospital from March 2012 to December 2018. Resistance trends were analysed per isolate and compared over the 7 year period.

Results

Among 1742 isolates, the most common samples were pus (53.4%), wound swabs (30.5%) and blood (6.9%). The most frequently detected bacteria from these sample types were Staphylococcus aureus (21.9%), Pseudomonas aeruginosa (20.9%) and Klebsiella pneumoniae (16.7%). MDR bacteria (32.0%), ESBL-producing bacteria (39.1%), MRSA (24.1%) and carbapenem-resistant Enterobacteriaceae (CRE) species (2.6%) were all detected. Between 2012 and 2018 the number of ESBL isolates significantly increased from 3.2% to 42.9% (P = 0.0001), and resistance to clindamycin in MSSA isolates rose from 3.7% to 29.6% (P = 0.003). Two critical WHO priority pathogens (ESBL-producing CRE and carbapenem-resistant P. aeruginosa) were also detected.

Conclusions

Over a 7 year period, a high prevalence of MDR bacteria was observed, while ESBL-producing bacteria showed a significantly increasing trend. ABR surveillance is important to inform clinical decisions, treatment guidelines and infection prevention and control practices.

Risk Factors for Acute Cholangitis Caused by Enterococcus faecalis and Enterococcus faecium

Background/Aims

Acute cholangitis (AC) is a potentially life-threatening bacterial infection, and timely antimicrobial treatment, faster than that achieved with bacterial cultures, is recommended. Although the current guidelines refer to empirical antimicrobial treatment, various kinds of antimicrobial agents have been cited because of insufficient analyses on the spectrum of pathogens in AC. Enterococcus spp. is one of the most frequently isolated Gram-positive bacteria from the bile of patients with AC, but its risk factors have not been extensively studied. This study aimed to analyze the risk factors of AC caused by Enterococcusfaecalis and Enterococcusfaecium.

Methods

Patients with AC who were hospitalized in a Japanese tertiary center between 2010 and 2015 were retrospectively analyzed. Patients’ first AC episodes in the hospital were evaluated.

Results

A total of 266 patients with AC were identified. E. faecalis and/or E. faecium was isolated in 56 (21%) episodes of AC. Prior endoscopic sphincterotomy (EST), the presence of a biliary stent, prior cholecystectomy, and past intensive care unit admission were more frequently observed in AC patients with E. faecalis and/or E. faecium than in those without such bacteria. Prior EST was identified as an independent risk factor for AC caused by E. faecalis and/or E. faecium in the multivariate analysis.

Conclusions

Given the intrinsic resistance of E. faecalis and E. faecium to antibiotics, clinicians should consider empirical therapy with anti-enterococcal antibiotics for patients with prior EST.

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

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

Diphenhydramine and levofloxacin combination therapy against antimicrobial resistance in respiratory tract infections

Background: Antibiotics are in use since decades to treat various infections caused by Gram-positive and Gram-negative bacteria such as Staphylococcus aureus and Pseudomonas aeruginosa. Diphenhydramine, an H1 receptor blocker possesses a weak antibiotic action but when combined with other antibiotics may potentiate their antibacterial activity. Materials & methods: This study investigated in vitro antibacterial activity of diphenhydramine when used alone and in combination with levofloxacin against methicillin-resistant S. aureus and P. aeruginosa. Results: The combined antibacterial effect of the drugs against bacteria showed a fractional inhibitory concentration index of ≤0.5, in other words, synergism. No cytotoxicity was observed as percentage cell viability was >50%. Conclusion: The combination of diphenhydramine and levofloxacin exerted antibacterial activity, and was not found to be cytotoxic when given in combination against P. aeruginosa and S. aureus.

Outcomes and Risk Factors in Prosthetic Joint Infections by multidrug-resistant Gram-negative Bacteria: A Retrospective Cohort Study

Gram-negative bacteria (GNB), including multidrug-resistant (MDR) pathogens, are gaining importance in the aetiology of prosthetic joint infection (PJI). This retrospective observational study identified independent risk factors (RFs) associated with MDR-GNB PJI and their influence on treatment outcomes. We assessed MDR bacteria causing hip and knee PJIs diagnosed at a Brazilian tertiary hospital from January 2014 to July 2018. RFs associated with MDR-GNB PJI were estimated by bivariate and multivariate analyses using prevalence ratios (PRs) with significance at p < 0.05. Kaplan–Meier analysis was performed to evaluate treatment outcomes. Overall, 98 PJI patients were analysed, including 56 with MDR-GNB and 42 with other bacteria. Independent RFs associated with MDR-GNB PJI were revision arthroplasty (p = 0.002), postoperative hematoma (p < 0.001), previous orthopaedic infection (p = 0.002) and early infection (p = 0.001). Extensively drug-resistant GNB (p = 0.044) and comorbidities (p = 0.044) were independently associated with MDR-GNB PJI treatment failure. In sum, MDR-GNB PJI was independently associated with previous orthopaedic surgery, postoperative local complications and pre-existing infections and was possibly related to selective pressure on bacterial skin colonisation by antibiotics prescribed for early PJI. Infections due to MDR-GNB and comorbidities were associated with higher treatment failure rates.

Antimicrobial resistance profiles of microorganisms isolated from hospitalized patients in Dominican Republic

Objective.

To define the antimicrobial resistance profiles of the microorganisms most commonly isolated from hospitalized adult patients in Dominican Republic (DR).

Methods.

A retrospective, cross-sectional study of phenotypic antimicrobial susceptibility patterns was conducted using data from 3 802 clinical microbiology reports specifying positive bacterial cultures in samples collected from patients admitted to the clinical, surgery, and intensive care units (ICU) at three tertiary-level care hospitals in the city of Santiago de los Caballeros from 1 January 2016 – 31 December 2017. Descriptive statistics and chi-square test (P ≤ 0.05) were used to analyze the qualitative variables.

Results.

At the three hospitals, there were 932, 1 090, and 1 780 microbiology reports analyzed. Of the total, 1274 were from the ICU, 1 042 from the surgery unit, and 1 486 from the clinical unit. Methicillin resistance was found in 57.3% of the Staphylococcus aureus isolates and 75.3% of the coagulase-negative staphylococci. Third-generation cephalosporin resistance was detected in 54.4% of isolates identified as members of the Enterobacteriaceae family, 67.3% of the Acinetobacter spp., and 91.7% of the Pseudomonas, while carbapenem resistance was shown by 8.0%, 23.8%, and 51.0% of these, respectively. Most of the resistant Acinetobacter spp. isolates were found in just one hospital and the prevalence of Enterobacteriaceae resistant to carbapenems was highest in the ICU.

Conclusion.

Antimicrobial resistance levels are high among hospitalized patients in Dominican Republic and may cause enhanced risk factors that impact clinical outcomes. Urgent measures are needed to address antimicrobial resistance in DR.

High Burden of Resistant Gram Negative Pathogens Causing Device-associated Healthcare Infections in a Tertiary Care Setting in Saudi Arabia, 2008-2016

OBJECTIVES

There is local and regional deficiency in the data examining the contribution of resistant pathogens to device-associated healthcare-associated infections (DA-HAIs). The objective was to examine such data in a multi-hospital system in Saudi Arabia in comparison with the US National Health Surveillance Network (NHSN).

METHODS

Surveillance of DA-HAIs was prospectively conducted between 2008 and 2016 in four hospitals of Ministry of National Guard Health Affairs. Consecutive NHSN reports were used for comparisons. Definitions and methodology of DA-HAIs and bacterial resistance were based on NHSN.

RESULTS

A total 1260 pathogens causing 1141 DA-HAI events were included. Gram negative pathogens (GNPs) were responsible for 62.5% of DA-HAIs, with a significantly higher Klebsiella, Pseudomonas, Acinetobacter, and Enterobacter than NHSN hospitals. Approximately 28.3% of GNPs and 23.5% of gram positive pathogens (GPPs) had some type of resistance. Nearly 34.3% of Klebsiella were resistant to third/fourth generation cephalosporins, 4.8% of Enterobacteriaceae were carbapenem-resistant (CRE), 24.4% of Staphylococcus aureus were methicillin-resistant (MRSA), and 21.9% of Enterococci were vancomycin-resistant (VRE). Multidrug resistance (MDR) was 65.0% in Acinetobacter, 26.4% in Escherichia coli, 23.0% in Klebsiella, and 14.9% in Pseudomonas. Resistant GNPs including cephalosporin-resistant Klebsiella, MDR Klebsiella, and MDR Escherichia coli were significantly more frequent while resistant GPPs including MRSA and VRE were significantly less frequent than NHSN hospitals.

CONCLUSION

The current findings showed heavier and more resistant contribution of GNPs to DA-HAIs in Saudi hospitals compared with American hospitals. The higher resistance rates in Klebsiella and Escherichia coli are alarming and call for effective antimicrobial stewardship programs.

Profile of Enterobacteria Resistant to Beta-Lactams

A serious emerging problem worldwide is increased antimicrobial resistance. Acquisition of coding genes for evasion methods of antimicrobial drug mechanisms characterizes acquired resistance. This phenomenon has been observed in Enterobacteriaceae family. Treatment for bacterial infections is performed with antibiotics, of which the most used are beta-lactams. The aim of this study was to correlate antimicrobial resistance profiles in Enterobacteriaceae by phenotypic methods and molecular identification of 14 beta-lactamase coding genes. In this study, 70 exclusive isolates from Brazil were used, half of which were collected in veterinary clinics or hospitals Phenotypic methodologies were used and real-time PCR was the molecular methodology used, through the Sybr Green system. Regargding the results found in the tests it was observed that 74.28% were resistant to ampicillin, 62.85% were resistant to amoxicillin associated with clavalunate. The mechanism of resistance that presented the highest expression was ESBL (17.14%). The genes studied that were detected in a greater number of species were blaGIM and blaSIM (66.66% of the samples) and the one that was amplified in a smaller number of samples was blaVIM (16.66%). Therefore, high and worrying levels of antimicrobial resistance have been found in enterobacteria, and a way to minimize the accelerated emergence of their resistance includes developing or improving techniques that generate diagnoses with high efficiency and speed.

Analysis of drug resistance of extended-spectrum beta-lactamases-producing Escherichia coli and Klebsiella pneumoniae in children with urinary tract infection

Objectives:

To investigate the drug resistance of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K.pneumoniae) in children with urinary tract infection (UTI) and to provide the rationale for clinical use of antibiotics.

Methods:

This is a retrospective analysis of drug susceptibility in children with E. coli or K. pneumoniae-positive urine culture between August 2013 and August 2017, Shenzhen Children’s Hospital, Shenzhen, China. Drug resistance was statistically assessed using Fisher exact test and χ² test.

Results:

A total of 698 cases of E. coli, 426 of which were confirmed ESBL-producing strains, and 217 cases of K. pneumoniae, including 111 ESBL-producing strains, were detected, and the difference in proportion of positive ESBL-producing strains (61.03% versus 51.15%) was statistically significant (p=0.010). The average drug resistance rates of E. coli and K. pneumoniae to piperacillin/tazobactam, meropenem, ertapenem, imipenem, and amikacin were <15%. The average resistance rates of ESBL-producing E. coli and K. pneumoniae to cefpodoxime, cefixime, cefazolin, and ceftriaxone was >98%, while average resistance rates for non-ESBL-producing bacteria to the above 4 drugs was <20%.

Conclusion:

In southern China, the proportion of ESBL-producing strains and the drug resistance rates of E. coli and K. pneumoniae in UTI in children was high, but their resistance rates to carbapenems and β-lactamase inhibitor complexes containing tazobactam were low. Carbapenems are the most effective antibacterial drugs for the treatment of ESBL-producing bacteria.

Global priority pathogens: virulence, antimicrobial resistance and prospective treatment options

Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Salmonella spp. are part of a group of pathogens that pose a major threat to human health due to the emergence of multidrug-resistant strains. Moreover, these bacteria have several virulence factors that allow them to successfully colonize their hosts, such as toxins and the ability to produce biofilms, resulting in an urgent need to develop new strategies to fight these pathogens. In this review, we compile the most up-to-date information on the epidemiology, virulence and resistance of these clinically important microorganisms. Additionally, we address new therapeutic alternatives, with a focus on molecules with antivirulence activity, which are considered promising to combat multidrug-resistant bacteria.

The global prevalence of Daptomycin, Tigecycline, Quinupristin/Dalfopristin, and Linezolid-resistant Staphylococcus aureus and coagulase-negative staphylococci strains: a systematic review and meta-analysis

Objective

Methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative Staphylococcus (MRCoNS) are among the main causes of nosocomial infections, which have caused major problems in recent years due to continuously increasing spread of various antibiotic resistance features. Apparently, vancomycin is still an effective antibiotic for treatment of infections caused by these bacteria but in recent years, additional resistance phenotypes have led to the accelerated introduction of newer agents such as linezolid, tigecycline, daptomycin, and quinupristin/dalfopristin (Q/D). Due to limited data availability on the global rate of resistance to these antibiotics, in the present study, the resistance rates of S. aureus, Methicillin-resistant S. aureus (MRSA), and CoNS to these antibiotics were collected.

Method

Several databases including web of science, EMBASE, and Medline (via PubMed), were searched (September 2018) to identify those studies that address MRSA, and CONS resistance to linezolid, tigecycline, daptomycin, and Q/D around the world.

Result

Most studies that reported resistant staphylococci were from the United States, Canada, and the European continent, while African and Asian countries reported the least resistance to these antibiotics. Our results showed that linezolid had the best inhibitory effect on S. aureus. Although resistances to this antibiotic have been reported from different countries, however, due to the high volume of the samples and the low number of resistance, in terms of statistical analyzes, the resistance to this antibiotic is zero. Moreover, linezolid, daptomycin and tigecycline effectively (99.9%) inhibit MRSA. Studies have shown that CoNS with 0.3% show the lowest resistance to linezolid and daptomycin, while analyzes introduced tigecycline with 1.6% resistance as the least effective antibiotic for these bacteria. Finally, MRSA and CoNS had a greater resistance to Q/D with 0.7 and 0.6%, respectively and due to its significant side effects and drug-drug interactions; it appears that its use is subject to limitations.

Conclusion

The present study shows that resistance to new agents is low in staphylococci and these antibiotics can still be used for treatment of staphylococcal infections in the world.

High prevalence of CTX-M-1 group in ESBL-producing enterobacteriaceae infection in intensive care units in southern Chile

Enterobacteria-producing extended-spectrum β-lactamases (ESBL) play an important role in healthcare infections, increasing hospitalization time, morbidity and mortality rates. Among several ESBLs that emerge from these pathogens, CTX-M-type enzymes had the most successful global spread in different epidemiological settings. Latin America presents high prevalence of CTX-M-2 in ESBL-producing enterobacterial infections with local emergence of the CTX-M-1 group. However, this high prevalence of the CTX-M-1 group has not yet been reported in Chile. The aim of this study was to identify ESBLs among enterobacteria isolated from clinical samples of critically ill patients from southern Chile. One-hundred thirty seven ESBL-producing bacteria were isolated from outpatients from all critical patient units from Hernán Henríquez Aravena Hospital. Phenotype characterization was performed by antibiogram, screening of ESBL, and determination of minimum inhibitory concentration (MIC). PCR was used for genetic confirmation of resistance. Molecular typing was performed by ERIC-PCR. ESBL-producing isolates were identified as Klebsiella pneumoniae (n = 115), Escherichia coli (n = 18), Proteus mirabilis (n = 3), and Enterobacter cloacae (n = 1), presenting multidrug resistance profiles. PCR amplification showed that the strains were positive for blaSHV (n = 111/81%), blaCTX-M-1 (n = 116/84.7%), blaTEM (n = 100/73%), blaCTX-M-2 (n = 28/20.4%), blaCTX-M-9 (0.7%), blaPER-1 (0.7%), and blaGES-10 (0.7%). The multiple production of ESBL was observed in 93% of isolates, suggesting high genetic mobility independent of the clonal relationship. The high frequency of the CTX-M-1 group and a high rate of ESBL co-production are changing the epidemiology of the ESBL profile in Chilean intensive care units. This epidemiology is a constant and increasing challenge, not only in Chile, but worldwide.

Virulence factors and integrons are associated with MDR and XDR phenotypes in nosocomial strains of Pseudomonas aeruginosa in a Venezuelan university hospital

Multidrug resistance (MDR), virulence and transferable elements potentiate Pseudomonas aeruginosa's role as an opportunistic pathogen creating a high risk for public health. In this study, we evaluated the possible association of multidrug resistance, virulence factors and integrons with intrahospital P. aeruginosa strains isolated from patients at Cumana hospital, Venezuela. Relevant clinical-epidemiological data were collected to study 176 strains (2009-2016) isolated from different hospital units. Bacterial resistance was classified as susceptible, low-level resistant (LDR), multidrug resistant (MDR) and extensively drug-resistant (XDR). Most strains produced pyoverdine, DNase, gelatinase and hemolysin. Around 73% of the strains showed some type of movement. MDR and XDR strains increased from 2009 (24.2% and 4.8%, respectively) to 2016 (53.1% and 18.8%); while LDR decreased from 64.5% to 6.3%. The exoU and exoS genes were found in a significant number of strains (38.1 and 7.4%, respectively). Class I integrons were detected in 35.8% of the strains and the frequency was associated with resistance (42.9, 22.4, 41.4 and 61.9%, for susceptible, LDR, MDR and XDR, respectively). The MDR/XDR strains were positively associated with hemolysins and exoU, but negatively associated with bacterial twitching. MDR/XDR phenotypes were also associated with the Intensive Care Unit (ICU), septicemia, bronchial infection and diabetic foot ulcers, as well as long hospital stay (≥10 days) and previous antimicrobial treatment. High frequency of MDR/XDR strains and their association with class I integrons and virulence factors can increase the infection potential, as well as morbidity and mortality of patients attending this hospital and could spread infection to the community, creating a health risk for the region.

The Enterococcus: a Model of Adaptability to Its Environment

The genus Enterococcus comprises a ubiquitous group of Gram-positive bacteria that are of great relevance to human health for their role as major causative agents of health care-associated infections. The enterococci are resilient and versatile species able to survive under harsh conditions, making them well adapted to the health care environment. Two species cause the majority of enterococcal infections: Enterococcus faecalis and Enterococcus faecium Both species demonstrate intrinsic resistance to common antibiotics, such as virtually all cephalosporins, aminoglycosides, clindamycin, and trimethoprim-sulfamethoxazole. Additionally, a remarkably plastic genome allows these two species to readily acquire resistance to further antibiotics, such as high-level aminoglycoside resistance, high-level ampicillin resistance, and vancomycin resistance, either through mutation or by horizontal transfer of genetic elements conferring resistance determinants.

Treating Surgical Infections in Low- and Middle-Income Countries: Source Control, Then What?

Surgical infections present a significant burden of disease globally. Management focuses on source control and appropriate antibiotic therapy. This remains a challenge in low- and middle-income settings, where access to surgical care and antibiotics is limited. This paper discusses the complex challenges facing the management of surgical infections in low- and middle-income countries.

Epidemiological characteristics and genetic structure of linezolid-resistant Enterococcus faecalis

Objectives

The aim of this study was to investigate the mechanism of linezolid resistance and evaluate the risk factors for linezolid-resistant Enterococcus faecalis (LZR-Efa) infections.

Methods

A total of 730 E. faecalis isolates were collected, and whole-genome sequencing and bioinformatics analysis were performed. Meanwhile, risk factors related to linezolid resistance were analyzed by binary logistic regression.

Results

Twenty-six LZR-Efa were isolated from various clinical samples, and 24 isolates were multidrug resistant. Four isolates were daptomycin nonsusceptible, while all LZR-Efa were susceptible to vancomycin. Thirteen different sequence types (STs) were identified, and the most prevalent type was ST16 (23.1%). The genes dfrE, lsaA, and emeA were identified in all isolates. A total of 23 E. faecalis were positive for optrA gene, and six amino acids mutations were identified among 18 LZR-Efa in OptrA. The 23S rRNA mutation was found in 16 LZR-Efa isolates. However, the presence of cfr was not identified. Furthermore, there were 41 virulence genes detected, and 10 genes (ace, bopD, cpsA, cpsB, ebpB, ebpC, efaA, fss1, fss2, and srtC) were found in all isolates. A total of nine isolates were positive for multiple virulent factors (ace, asa1, cylA, efaA, esp, and gelE). There was no difference in the number of virulence factors among different specimens (P=0.825). It is of note that all patients had not been prescribed linezolid or traveled abroad previously. Moreover, previous use of carbapenems was a risk factor for LZR-Efa infections.

Conclusion

The main trends of LZR-Efa, with lower level of resistance, were sporadic mainly in the department of surgery. optrA and 23S rRNA were the main resistance mechanisms. In addition, carbapenems use was an independent predictor of LZR-Efa infections.

Molecular basis for the emergence of a new hospital endemic tigecycline-resistant Enterococcus faecalis ST103 lineage

Enterococcus faecalis are a major cause of nosocomial infection worldwide, and the spread of vancomycin resistant strains (VRE) limits treatment options. Tigecycline-resistant VRE began to be isolated from inpatients at a Brazilian hospital within months following the addition of tigecycline to the hospital formulary. This was found to be the result of a spread of an ST103 E. faecalis clone. Our objective was to identify the basis for tigecycline resistance in this lineage. The genomes of two closely related tigecycline-susceptible (MIC = 0.06 mg/L), and three representative tigecycline-resistant (MIC = 1 mg/L) ST103 isolates were sequenced and compared. Further, efforts were undertaken to recapitulate the emergence of resistant strains in vitro. The specific mutations identified in clinical isolates in several cases were within the same genes identified in laboratory-evolved strains. The contribution of various polymorphisms to the resistance phenotype was assessed by trans-complementation of the wild type or mutant alleles, by testing for differences in mRNA abundance, and/or by examining the phenotype of transposon insertion mutants. Among tigecycline-resistant clinical isolates, five genes contained non-synonymous mutations, including two genes known to be related to enterococcal tigecycline resistance (tetM and rpsJ). Finally, within the in vitro-selected resistant variants, mutation in the gene for a MarR-family response regulator was associated with tigecycline resistance. This study shows that E. faecalis mutates to attain tigecycline resistance through the complex interplay of multiple mechanisms, along multiple evolutionary trajectories.

Nosocomial outbreaks caused by Acinetobacter baumannii and Pseudomonas aeruginosa: Results of a systematic review

BACKGROUND

Large outbreaks of infection by Acinetobacter baumannii and Pseudomonas aeruginosa have been reported. This research compares characteristics of such outbreaks.

OBJECTIVES

Determination of risk factors for the occurrence and appropriate infection control measures.

DATA SOURCES

The Outbreak Database, PubMed, and reference lists of identified articles were used. Key words included nosocomial and (outbreak or epidemic) and (aeruginosa or baumannii).

STUDY ELIGIBILITY CRITERIA

Articles were included if they describe distinct outbreak(s) caused by A baumannii or P aeruginosa and were published between 2000 and 2015. There were no further restrictions with respect to language or type of article.

RESULTS

One hundred fifty outbreaks by A baumannii and 131 outbreaks by P aeruginosa were included, including multidrug-resistant strains in 113 Acinetobacter and 49 Pseudomonas outbreaks. Acinetobacter outbreaks were mainly reported from intensive care units, after use of antibiotics, during mechanical ventilation, and presented with a mortality rate of 47% compared with 23% by Pseudomonas. Resistance did not alter mortality by either species. Most infection control measures were implemented or enforced more often in Acinetobacter outbreaks.

CONCLUSIONS

These findings should support staff in infection control departments and on wards if an outbreak is suspected. Better adherence to the Outbreak Reports and Intervention Studies of Nosocomial Infection guidelines in outbreak reporting is necessary. A precise definition of multidrug resistance for Acinetobacter and Pseudomonas is lacking.