Antibiotic regimens and intestinal colonization with antibiotic-resistant gram-negative bacilli

Hospital-acquired bloodstream infections in patients with cancer: current knowledge and future directions

Patients with cancer experience higher rates of preventable harm from hospital-acquired bloodstream infections (haBSIs) and central-line-associated bloodstream infections (CLABSIs) compared with the general hospital population. The prevention of haBSIs and CLABSIs in patients with cancer is an urgent priority, and requires standardized surveillance and reporting efforts. The application of haBSI and CLABSI definitions, classification systems and surveillance strategies for patients with cancer is complex, and there is wide variation in clinical practice. Existing systems were not designed explicitly for patients with cancer, and have different strengths and weaknesses in the cancer setting. For these reasons, epidemiological estimates of haBSIs and CLABSIs in patients with cancer also require careful interpretation. This complexity can be a barrier to identifying appropriate targets for intervention and reducing preventable harm. This review provides an overview of key concepts and challenges in haBSI surveillance and prevention specific to patients with cancer. In addition, this review summarizes the strengths and weaknesses of commonly used surveillance definitions and denominators in the setting of cancer care; existing surveillance practice; epidemiology of haBSIs and CLABSIs; prevention strategies; and current knowledge gaps. A global collaborative effort to harmonize the surveillance of hospital-acquired infections in patients with cancer would be invaluable to improve the accuracy and utility of existing data, advance efforts to prevent hospital-acquired infections, and improve patient safety.

Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action

Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice.

Acinetobacter Metabolism in Infection and Antimicrobial Resistance

Acinetobacter infections have high rates of mortality due to an increasing incidence of infections by multidrug-resistant (MDR) and extensively-drug-resistant (XDR) strains. Therefore, new therapeutic strategies for the treatment of Acinetobacter infections are urgently needed. Acinetobacter spp. are Gram-negative coccobacilli that are obligate aerobes and can utilize a wide variety of carbon sources. Acinetobacter baumannii is the main cause of Acinetobacter infections, and recent work has identified multiple strategies A. baumannii uses to acquire nutrients and replicate in the face of host nutrient restriction. Some host nutrient sources also serve antimicrobial and immunomodulatory functions. Hence, understanding Acinetobacter metabolism during infection may provide new insights into novel infection control measures. In this review, we focus on the role of metabolism during infection and in resistance to antibiotics and other antimicrobial agents and discuss the possibility that metabolism may be exploited to identify novel targets to treat Acinetobacter infections.

Iron in infectious diseases friend or foe?: The role of gut microbiota

Iron is a trace element involved in metabolic functions for all organisms, from microorganisms to mammalians. Iron deficiency is a prevalent health problem that affects billions of people worldwide, and iron overload could have some hazardous effect. The complex microbial community in the human body, also called microbiota, influences the host immune defence against infections. An imbalance in gut microbiota, dysbiosis, changes the host's susceptibility to infections by regulating the immune system. In recent years, the number of studies on the relationship between infectious diseases and microbiota has increased. Gut microbiota is affected by different parameters, including mode of delivery, hygiene habits, diet, drugs, and plasma iron levels during the lifetime. Gut microbiota may influence iron levels in the body, and iron overload and deficiency can also affect gut microbiota composition. Novel researches on microbiota shed light on the fact that the bidirectional interactions between gut microbiota and iron play a role in the pathogenesis of many diseases, especially infections. A better understanding of these interactions may help us to comprehend the pathogenesis of many infectious and metabolic diseases affecting people worldwide and following the development of more effective preventive and/or therapeutic strategies. In this review, we aimed to present the iron-mediated host-gut microbiota interactions, susceptibility to bacterial infections, and iron-targeted therapy approaches for infections.

Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae

Infections by multidrug-resistant Enterobacteriaceae (MRE) are life-threatening to patients. The intestinal microbiome protects against MRE colonization, but antibiotics cause collateral damage to commensals and open the way to colonization and subsequent infection. Despite the significance of this problem, the specific commensals and mechanisms that restrict MRE colonization remain largely unknown. Here, by performing a multi-omic prospective study of hospitalized patients combined with mice experiments, we find that Lactobacillus is key, though not sufficient, to restrict MRE gut colonization. Lactobacillus rhamnosus and murinus increase the levels of Clostridiales bacteria, which induces a hostile environment for MRE growth through increased butyrate levels and reduced nutrient sources. This mechanism of colonization resistance, an interaction between Lactobacillus spp. and Clostridiales involving cooperation between microbiota members, is conserved in mice and patients. These results stress the importance of exploiting microbiome interactions for developing effective probiotics that prevent infections in hospitalized patients.

Multidrug-resistant Enterobacteriaceae (MRE) represent a major threat for patients’ health. Here, the authors describe how cooperation between gut commensal bacteria (Lactobacillus spp. And Clostridiales) restrict MRE colonization in mice and patients

Characteristics of Escherichia coli Isolated from Intestinal Microbiota Children of 0–5 Years Old in the Commune of Abomey-Calavi

Escherichia coli is a commensal bacterium and one of the first bacteria to colonize the digestive tract of newborns after birth. It is characterized by great versatility and metabolic flexibility that allows its survival in different niches. The present study aims at analyzing the diversity of E. coli strains isolated from the intestinal microbiota of children aged from 0 to 5 years in the commune of Abomey-Calavi in Benin. For this purpose, a descriptive and analytical cross-sectional study was conducted. A total of 135 stool samples were collected from the pediatric clinic of Abomey-Calavi. Microbiological analyses were performed according to standard microbiology analytical techniques. The molecular characterization of E. coli was performed by investigating eight genes (dinB, icdA, pabB, polB, putP, trpA, trpB, and uidA) using the PCR technique. The results showed that the average loading rate on stool samples was 3.74 × 107 CFU/g for TAMF. A total of 7 species of bacteria were identified at different proportions: Staphylococcus spp (55.36%), E. coli (14.29%), Klebsiella ornithinolytica (12.5%), Serratia odorifera (5.36%), and Enterobacter aerogenes (5.36%). Interestingly, isolated E. coli presented a resistance of 100% to cefotaxime and aztreonam. In addition, resistances of 95.24% and 50% were observed against erythromycin and nalidixic acid, respectively. The molecular characterization of the isolated E. coli strains allowed us to discover another molecular variation within the isolated strains. Genes encoding the enzymes isocitrate dehydrogenase (icd) and DNA polymerase II (polB) were detected at 96.30% in the isolated E. coli strains. Moreover, the genes encoding the enzymes beta-D-glucuronidase (uidA) and DNA polymerase (dinB) were detected at 88.89% in the isolated E. coli strains. Interestingly, 81.48%, 85.19, 92.59%, and 100% of isolated E. coli strains expressed the genes encoding the enzymes tryptophan synthase subunit A (trpA), proline permease (putP), p-aminobenzoate synthase, and tryptophan synthase subunit B (trpB), respectively. The diversity of E. coli strains reflects the importance of regulatory mechanisms in the adaptation of bacteria to the gut microbiota.

Evaluation and Management of Traveler's Diarrhea in Children

Traveler's diarrhea is the most common travel disease in both children and adults. Adult guidelines for traveler's diarrhea have been established, but significant gaps persist in guidance for the evaluation and management of pediatric traveler's diarrhea. Adult guidelines are not necessarily applicable in children, and it is essential for clinicians to account for the differences in pediatric pathophysiology, clinical presentations, and treatment recommendations when evaluating and managing pediatric traveler's diarrhea.

Antibiotic exposure and acquisition of antibiotic-resistant gram-negative bacteria among outpatients at a US Veterans Affairs medical center

Objectives:

To assess the prevalence of antibiotic-resistant gram-negative bacteria (R-GNB) among patients without recent hospitalization and to examine the influence of outpatient antibiotic exposure on the risk of acquiring R-GNB in this population.

Design:

2-year retrospective cohort study.

Setting:

Regional Veterans Affairs healthcare system.

Patients:

Outpatients at 13 community-based clinics.

Methods:

We examined the rate of acquisition of R-GNB within 90 days following an outpatient visit from 2018 to 2019. We used clinical and administrative databases to determine and summarize prescriptions for systemic antibiotics, associated infectious diagnoses, and subsequent R-GNB acquisition among patients without recent hospitalizations. We also calculated the odds ratio of R-GNB acquisition following antibiotic exposure.

Results:

During the 2-year study period, 7,215 patients had outpatient visits with microbiological cultures obtained within 90 days. Of these patients, 206 (2.9%) acquired an R-GNB. Among patients receiving antibiotics at the visit, 4.6% acquired a R-GNB compared to 2.7% among patients who did not receive antibiotics, yielding an unadjusted odds ratio of 1.75 (95% confidence interval, 1.18–2.52) for a R-GNB following an outpatient visit with versus without an antibiotic exposure. Regardless of R-GNB occurrence, >50% of antibiotic prescriptions were issued at visits without an infectious disease diagnosis or issued without documentation of an in-person or telehealth clinical encounter.

Conclusions:

Although the rate of R-GNBs was low (2.9%), the 1.75-fold increased odds of acquiring a R-GNB following an outpatient antibiotic highlights the importance of antimicrobial stewardship efforts in outpatient settings. Specific opportunities include reducing antibiotics prescribed without an infectious diagnosis or a clinical visit.

Prolonged carriage of ESBL-producing enterobacterales and potential cross-transmission among residents in geriatric long-term care facilities

Previous studies indicated residents in geriatric long-term care facilities (LTCFs) had much higher prevalence of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) carriage than the general population. Most ESBL-E carriers are asymptomatic. The study tested the hypothesis that residents with ESBL-E carriage may accumulate inside geriatric LTCFs through potential cross-transmission after exposure to residents with prolonged ESBL-E carriage. 260 residents from four Japanese LTCFs underwent ESBL-E testing of fecal specimens and were divided into two cohorts: Cohort 1,75 patients with ≥ 2 months residence at study onset; Cohort 2, 185 patients with < 2 months residence at study onset or new admission during the study period. Three analyses were performed: (1) ESBL-E carriage statuses in Cohort 1 and Cohort 2; (2) changes in ESBL-E carriage statuses 3-12 months after the first testing and ≥ 12 months after the second testing; and (3) lengths of positive ESBL-E carriage statuses. Compared with the residents in Cohort 1, a significantly larger proportion of residents in Cohort 2 were positive for ESBL-E carriage (28.0% in Cohort 1 vs 40.0% in Cohort 2). In the subsequent testing results, 18.3% of residents who were negative in the first testing showed positive conversion to ESBL-E carriage in the second testing, while no patients who were negative in the second testing showed positive conversion in the third testing. The maximum length of ESBL-E carriage was 17 months. The findings indicated that some residents acquired ESBL-E through potential cross-transmission inside the LTCFs after short-term residence. However, no residents showed positive conversion after long-term residence, which indicates that residents with ESBL-E carriage may not accumulate inside LTCFs. Practical infection control and prevention measures could improve the ESBL-E prevalence in geriatric LTCFs.

Role of AmpG in the resistance to β-lactam agents, including cephalosporins and carbapenems: candidate for a novel antimicrobial target

BACKGROUND

A complex cascade of genes, enzymes, and transcription factors regulates AmpC β-lactamase overexpression. We investigated the network of AmpC β-lactamase overexpression in Klebsiella aerogenes and identified the role of AmpG in resistance to β-lactam agents, including cephalosporins and carbapenems.

METHODS

A transposon mutant library was created for carbapenem-resistant K. aerogenes YMC2008-M09-943034 (KE-Y1) to screen for candidates with increased susceptibility to carbapenems, which identified the susceptible mutant derivatives KE-Y3 and KE-Y6. All the strains were subjected to highly contiguous de novo assemblies using PacBio sequencing to investigate the loss of resistance due to transposon insertion. Complementation and knock-out experiments using lambda Red-mediated homologous recombinase and CRISPR-Cas9 were performed to confirm the role of gene of interest.

RESULTS

In-depth analysis of KE-Y3 and KE-Y6 revealed the insertion of a transposon at six positions in each strain, at which truncation of the AmpG permease gene was common in both. The disruption of the AmpG permease leads to carbapenem susceptibility, which was further confirmed by complementation. We generated an AmpG permease gene knockout using lambda Red-mediated recombineering in K. aerogenes KE-Y1 and a CRISPR-Cas9-mediated gene knockout in multidrug-resistant Klebsiella pneumoniae-YMC/2013/D to confer carbapenem susceptibility.

CONCLUSIONS

These findings suggest that inhibition of the AmpG is a potential strategy to increase the efficacy of β-lactam agents against Klebsiella aerogenes.

Change in hospital antibiotic use and acquisition of multidrug-resistant gram-negative organisms after the onset of coronavirus disease 2019

Interrupted time series segmented regression was conducted to trend antibiotic use and multidrug-resistant gram-negative (MDRGN) acquisition relative to COVID-19 in an academic hospital. Total antibiotic use and antibiotic use related to pneumonia was higher in the period after the onset of COVID-19 compared to the similar calendar period in 2019. Furthermore, MDRGN acquisition increased 3% for every increase in positive COVID-19 tests per week.

Gastrointestinal Microbiota Disruption and Risk of Colonization With Carbapenem-resistant Pseudomonas aeruginosa in Intensive Care Unit Patients

BACKGROUND

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) colonizes the gastrointestinal tract of intensive care unit (ICU) patients, and CRPA colonization puts patients at increased risk of CRPA infection. Prior studies have not examined relationships between the microbiota, medications, and CRPA colonization acquisition.

METHODS

Data and perirectal swabs were obtained from a cohort of ICU patients at the University of Maryland Medical Center. Patients (N = 109) were classified into 3 groups by CRPA colonization-acquisition status and antimicrobial exposure. We conducted 16S ribosomal RNA gene sequencing of an ICU admission swab and ≥1 additional swab and evaluated associations between patient characteristics, medications, the gastrointestinal microbiota, and CRPA colonization acquisition.

RESULTS

ICU patients had low levels of diversity and high relative abundances of pathobionts. Piperacillin-tazobactam was prescribed more frequently to patients with CRPA colonization acquisition than those without. Piperacillin-tazobactam was associated with low abundance of potentially protective taxa (eg, Lactobacillus and Clostridiales) and increased risk of Enterococcus domination (odds ratio [OR], 5.50; 95% confidence interval [CI], 2.03-14.92). Opioids were associated with dysbiosis in patients who did not receive antibiotics; potentially protective Blautia and Lactobacillus were higher in patients who did not receive opioids. Several correlated taxa, identified at ICU admission, were associated with lower risk of CRPA colonization acquisition (OR, 0.58; 95% CI, .38-.87).

CONCLUSIONS

Antibiotics differed in their impact on the microbiota, with piperacillin-tazobactam being particularly damaging. Certain bacterial taxa (eg, Clostridiales) were negatively associated with CRPA colonization acquisition. These taxa may be markers of risk for CRPA colonization acquisition and/or serve a protective role.

Therapeutic Potential of the Gut Microbiota in the Management of Sepsis

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2020. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2020. Further information about the Annual Update in Intensive Care and Emergency Medicine is available from http://www.springer.com/series/8901.

Improving Risk-Benefit in Faecal Transplantation through Microbiome Screening

Faecal microbiota transplantation (FMT) has been shown to be effective in the treatment of a growing number of conditions, and its clinical use continues to rise. However, recent cases of antibiotic-resistant pathogen transmission through FMT, resulting in at least one case of fatal sepsis, highlight the need to reevaluate current donor screening practices. Commensal gut microbes profoundly influence infection risk but are not routinely assessed in donor stool. Extending the assessment of donor material beyond pathogen populations to include the composition and structure of the wider faecal microbiota has the potential to reduce infectious complications in FMT recipients.

Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae

Metagenomic sequencing of fecal DNA can usefully characterise an individual's intestinal resistome but is limited by its inability to detect important pathogens that may be present at low abundance, such as carbapenemase or extended-spectrum beta-lactamase producing Enterobacteriaceae. Here we aimed to develop a hybrid protocol to improve detection of resistance genes in Enterobacteriaceae by using a short period of culture enrichment prior to sequencing of DNA extracted directly from the enriched sample. Volunteer feces were spiked with carbapenemase-producing Enterobacteriaceae and incubated in selective broth culture for 6 hours before sequencing. Different DNA extraction methods were compared, including a plasmid extraction protocol to increase the detection of plasmid-associated resistance genes. Although enrichment prior to sequencing increased the detection of carbapenemase genes, the differing growth characteristics of the spike organisms precluded accurate quantification of their concentration prior to culture. Plasmid extraction increased detection of resistance genes present on plasmids, but the effects were heterogeneous and dependent on plasmid size. Our results demonstrate methods of improving the limit of detection of selected resistance mechanisms in a fecal resistome assay, but they also highlight the difficulties in using these techniques for accurate quantification and should inform future efforts to achieve this goal.

Risk factors for community acquired urinary tract infections caused by extended spectrum β-lactamase (ESBL) producing Escherichia coli in children: a case control study

Background: We noted a recent increase in cases of urinary tract infection due to community-acquired ESBL-producing Escherichia coli in children treated at our institution. Risk factors of urinary tract infection due to ESBL-producing E. coli in children in the USA remain unclear. Methods: A single center retrospective case control study of UTI due to CA-ESBL-producing E. coli during a 5-year period (2012-2016). Control cases with non-ESBL-producing E. coli urinary tract infection were matched by age, gender and year of infection. Results: A total of 111 patients with ESBL-producing E coli urinary tract infection and 103 controls were included. The proportion of ESBL-producing E coli urinary tract infection ranged from 7% to 15% of all UTI cases. The distribution of ESBL cases per year: 27 in 2012; 18 in 2013; 22 in 2014; 15 in 2015 and 29 in 2016. Median age was 4 years with female predominance (84%). The ESBL group was predominantly African American (32%) followed by individuals of Middle Eastern ethnic background (31%). Risk factors by univariate analysis were vesicoureteral reflux: (20.9 ESBL group vs 6% controls; p = .002), prior antibiotic usage in the last 3 months (including β-lactams), prior UTI (last 3 months), recent hospitalization (last 3 months) and Middle Eastern ethnic background. However, multivariate analysis showed that only prior antibiotic usage (p = .001) and Middle Eastern ethnic background (p < .001) were independent risk factors. ESBL-producing strains were more frequently resistant to trimethoprim-sulfamethoxazole (72% vs 25%) and ciprofloxacin (73% vs 5%) than strains not producing ESBL. Conclusion: Risk factors for community-acquired ESBL-producing E coli urinary tract in our pediatric patient population were antibiotic usage within the previous 3 months and Middle Eastern ethnic background. This may be related to increased risk of intestinal colonization with resistant bacterial strains.

Risk factors for acquisition and mortality of multidrug-resistant Acinetobacter baumannii bacteremia: A retrospective study from a Chinese hospital

Bloodstream infection caused by Acinetobacter baumannii has become a major clinical concern, especially multidrug-resistant A baumannii (MDRAB). The aim of this study was to identify the risk factors of nosocomial acquired MDRAB bacteremia and to determine the risk factors related to the mortality of patients with MDRAB bacteremia. Patients with nosocomial acquired A baumannii bacteremia were enrolled between January, 2013 and December, 2017 at the First Affiliated Hospital, School of Medicine, Zhejiang University. Medical records were reviewed, and the clinical and microbial characteristics were collected. Among the 338 patients suffering from A baumannii bacteremia, 274 patients were infected with MDRAB bacteremia. Bacteremia-related mortality was 46.4% for the overall sample; 56.2% for MDRAB bacteremia patients, 4.7% for non-MDRAB bacteremia patients. The identified risk factors for developing MDRAB bacteremia were previous exposure to carbapenems [odds ratio (OR) 5.78, P = .005] and penicillins+β-lactamase inhibitors (OR 4.29, P = .009). Primary bacteremia tended to develop non-MDR bacteremia (OR 0.10, P = .002). The risk factors for MDRAB bacteremia-related mortality were old age (OR 1.02, P = .036), a high Pitt bacteremia score (OR 1.32, P < .001), bacteremia occurring after severe pneumonia (OR 8.66, P < .001), while catheter-related infection (OR 0.47, P = .049) and operations for treating infection (OR 0.51, P = .043) may have a better outcome. Patients with MDRAB had a higher mortality rate. Patients with previous carbapenems and penicillins+β-lactamase inhibitor exposure are at an increased risk of MDRAB bacteremia, whereas patients with primary bacteremia tended to develop non-MDR bacteremia. The risk factors for MDRAB bacteremia-related mortality were old age, a high Pitt bacteremia score, and bacteremia occurring after severe pneumonia, whereas catheter-related infection and operations for the treatment of infection may have a better outcome.

Selection of ESBL-Producing E. coli in a Mouse Intestinal Colonization Model

Asymptomatic human carriage of antimicrobially drug-resistant pathogens prior to infection is increasing worldwide. Further investigation into the role of this fecal reservoir is important for combatting the increasing antimicrobial resistance problems. Additionally, the damage on the intestinal microflora due to antimicrobial treatment is still not fully understood. Animal models are powerful tools to investigate bacterial colonization subsequent to antibiotic treatment. In this chapter we present a mouse-intestinal colonization model designed to investigate how antibiotics select for an ESBL-producing E. coli isolate. The model can be used to study how antibiotics with varying effect on the intestinal flora promote the establishment of the multidrug-resistant E. coli. Colonization is successfully investigated by sampling and culturing stool during the days following administration of antibiotics. Following culturing, a precise identification of the bacterial strain found in mice feces is applied to ensure that the isolate found is in fact identical to the strain used for inoculation. For this purpose random amplified of polymorphic DNA (RAPD) PCR specifically developed for E. coli is applied. This method allows us to distinguish E. coli with more than 99.95% genome similarity using a duplex PCR method.

Alarming levels of antimicrobial resistance among sepsis patients admitted to ICU in a tertiary care hospital in India - a case control retrospective study

Background

Hospital acquired infections (HAI) are principal threats to the patients of intensive care units. An increase in the antimicrobial resistance (AMR) observed in gram negative bacteria is a great challenge to deal with. HAI and AMR lead to prolonged hospitalization and additional doses of anti-microbial treatment affecting patient's fitness and finances. Present study was undertaken to determine the pathotypes, genetic diversity and the antimicrobial resistance of E.coli in isolates from the patients admitted to intensive care unit at a tertiary care hospital in Delhi, India.

Methods

E.coli isolates (N = 77) obtained from the blood culture of patients diagnosed with sepsis and the isolates (N = 71) from the stool culture of patients admitted in intensive care unit (ICU) but not diagnosed with sepsis were investigated for their pathotypes, adherence patterns and genetic diversity by Enterobacterial Repeated Intergenic Consensus-polymerase chain reaction (ERIC-PCR). A Kirby-Bauer Disc diffusion test and antimicrobial susceptibility assays were performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Extended-spectrum β-lactamase (ESBL) genes and sequence type 131 (ST131) clone were characterised genotypically by gene-specific PCRs.

Results

Pathotypes analysis revealed 46 and 16% of the blood E.coli isolates were ETEC and EAEC respectively, in contrast to the fecal isolates wherein 22% of the isolates were ETEC and 28.5% were EAEC. EPEC, STEC and EIEC pathotypes were not detected in blood or fecal isolates. Of all the isolates studied, more than 90% of the blood and 70% of the fecal isolates were found to be resistant to cephalosporins. On the other hand, 68% of blood and 44% of the fecal isolates were found to be ESBL producers. Interestingly 83% of the blood isolates contained CTX-M15, whereas only 21% of them contained CTX-M9 genes. On the other hand CTX-M15 genes were found in 90% and CTX-M9 genes were found in 63% of the fecal isolates.

Conclusion

The antimicrobial resistant profile found in this study is alarming and poses a great threat to public health. Apparently an increased antimicrobial resistance to the extensively used cephalosporins is affecting an optimal drug therapy for patients. In addition, the presence of catheters, prolonged duration of stay in the hospital and poor hygienic conditions due to infrequent urination of the patient can lead to an additional vulnerability. Therefore continuous surveillance and rational use of antibiotics along with effective hygienic measures are urgently recommended in such settings.

Antibiotic resistance trends of ESKAPE pathogens in Kwazulu-Natal, South Africa: A five-year retrospective analysis

Background

To combat antimicrobial resistance, the World Health Organization developed a global priority pathogen list of antibiotic-resistant bacteria for prioritisation of research and development of new, effective antibiotics.

Objective

This study describes a five-year resistance trend analysis of the ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp., from Kwazulu-Natal, South Africa.

Methods

This retrospective study used National Health Laboratory Services data on 64 502 ESKAPE organisms isolated between 2011 and 2015. Susceptibility trends were ascertained from minimum inhibitory concentrations and interpreted using Clinical and Laboratory Standards Institute guidelines.

Results

S. aureus was most frequently isolated (n = 24, 495, 38%), followed by K. pneumoniae (n = 14, 282, 22%). Decreasing rates of methicillin-resistant S. aureus (28% to 18%, p < 0.001) and increasing rates of extended spectrum beta-lactamase producing K. pneumoniae (54% to 65% p < 0.001) were observed. Carbapenem resistance among K. pneumoniae and Enterobacter spp. was less than 6% during 2011–2014, but increased from 4% in 2014 to 16% in 2015 (p < 0.001) among K. pneumoniae. P. aeruginosa increased (p = 0.002), but resistance to anti-pseudomonal antimicrobials decreased from 2013 to 2015. High rates of multi-drug resistance were observed in A. baumanni (> 70%).

Conclusion

This study describes the magnitude of antimicrobial resistance in KwaZulu-Natal and provides a South African perspective on antimicrobial resistance in the global priority pathogen list, signalling the need for initiation or enhancement of antimicrobial stewardship and infection control measures locally.

Ventilator-associated pneumonia related to ESBL-producing gram negative bacilli

Ventilator-associated pneumonia (VAP) is one of the most frequent cause of intensive care unit (ICU) acquired infections. The worldwide spreading of extended spectrum beta-lactamase producing enterobacteriaceae (ESBL-PE) represents a major problem encountered more and more frequently in ICU. Among ICU patients, between 5% to 25% are ESBL-PE carriers. Whereas, previous carriage is the major risk factors associated with VAP related to ESBL-PE, among carriers, only 5% to 20% will develop a VAP related to ESBL-PE. Also, diagnosis and therapeutic delay are associated with length of stay and higher morbidity, and mortality, therefore, early identification of patients at risk of ESBL-PE related infections is crucial for early implementation of effective antibiotic therapy. VAP related to ESBL-PE should be considered in: previous colonized patients in case of late onset pneumonia and/or when several antibiotic courses precede the infectious episode or even in patients with shock. Among non-colonized patients, if VAP occurs, the risk being related to ESBL-PE is less than 1%. In the future, new rapid microbiological diagnostic tests will allow an early diagnosis. According to recent data, empirical antibiotic therapy should be based on carbapenems. Other alternative antibiotic classes could be used for de-escalation. However, several pharmacodynamic and pharmacokinetics precautions should be taken to achieve drug concentrations at site of infection and except to cure the infected patient.

Transmission of resistant Gram-negative bacteria to healthcare personnel gowns and gloves during care of residents in community-based nursing facilities

OBJECTIVE

To estimate the risk of transmission of antibiotic-resistant Gram-negative bacteria (RGNB) to gowns and gloves worn by healthcare personnel (HCP) when providing care to residents of community-based nursing facilities to identify the types of care and resident characteristics associated with transmission.

DESIGN

Prospective observational study.Settings and participantsResidents and HCP from 13 community-based nursing facilities in Maryland and Michigan.

METHODS

Perianal swabs were collected from residents and cultured to detect RGNB. HCP wore gowns and gloves during usual care activities, and at the end of each interaction, these were swabbed in a standardized manner. Transmission of RGNB from a colonized resident to gowns and gloves was estimated. Odds ratios (ORs) of transmission associated with type of care or resident characteristic were calculated.

RESULTS

We enrolled 403 residents and their HCP in this study. Overall, 19% of enrolled residents with a perianal swab (n=399) were colonized with at least 1 RGNB. RGNB transmission to either gloves or gowns occurred during 11% of the 584 interactions. Showering the resident, hygiene or toilet assistance, and wound dressing changes were associated with a high risk of transmission. Glucose monitoring and assistance with feeding or medication were associated with a low risk of transmission. Residents with a pressure ulcer were 3 times more likely to transmit RGNB than residents without one (OR, 3.3; 95% confidence interval [CI], 1.0-11.1).

CONCLUSIONS

Gown and glove use in community nursing facilities should be prioritized for certain residents and care interactions that are deemed a high risk for transmission.

Drug-resistant Enterobacteriaceae colonization is associated with healthcare utilization and antimicrobial use among inpatients in Pune, India

Background

Healthcare exposure may increase drug-resistant Enterobacteriaceae colonization risk. Nascent antimicrobial stewardship efforts in low- and middle-income countries require setting-specific data. We aimed to evaluate risk factors for inpatient drug resistant Enterobacteriaceae colonization in a resource-limited setting in India.

Methods

Patients age ≥ 6 months admitted with ≥24 h of fever to a tertiary hospital in Pune, India were enrolled in a prospective cohort. Perirectal swabs, collected on admission and hospitalization day 3 or 4, were cultured in vancomycin- and ceftriaxone-impregnated media to assess for ceftriaxone-resistant Enterobacteriaceae (CTRE) and carbapenem-resistant Enterobacteriaceae (CPRE). Multivariable analyses assessed risk factors for drug-resistant Enterobacteriaceae colonization among participants without admission colonization.

Results

Admission perirectal swabs were collected on 897 participants; 87 (10%) had CTRE and 14 (1.6%) had CPRE colonization. Admission CTRE colonization was associated with recent healthcare contact (p < 0.01). Follow-up samples were collected from 620 participants, 67 (11%) had CTRE and 21 (3.4%) had CPRE colonization. Among 561 participants without enrollment CTRE colonization, 49 (9%) participants were colonized with CTRE at follow-up. Detection of CTRE colonization among participants not colonized with CTRE at admission was independently associated with empiric third generation cephalosporin treatment (adjusted odds ratio [OR] 2.9, 95% CI 1.5–5.8). Follow-up transition to CPRE colonization detection was associated with ICU admission (OR 3.0, 95% CI 1.0–8.5).

Conclusions

Patients who receive empiric third generation cephalosporins and are admitted to the ICU rapidly develop detectable CTRE and CPRE colonization. Improved antimicrobial stewardship and infection control measures are urgently needed upon hospital admission.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3390-4) contains supplementary material, which is available to authorized users.

Hospital-acquired colonization and infections in a Vietnamese intensive care unit

Data concerning intensive care unit (ICU)-acquired bacterial colonization and infections are scarce from low and middle-income countries (LMICs). ICU patients in these settings are at high risk of becoming colonized and infected with antimicrobial-resistant organisms (AROs). We conducted a prospective observational study at the Ho Chi Minh City Hospital for Tropical Diseases, Vietnam from November 2014 to January 2016 to assess the ICU-acquired colonization and infections, focusing on the five major pathogens in our setting: Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), Klebsiella spp., Pseudomonas spp. and Acinetobacter spp., among adult patients with more than 48 hours of ICU stay. We found that 61.3% (223/364) of ICU patients became colonized with AROs: 44.2% (161/364) with rectal ESBL-producing E. coli and Klebsiella spp.; 30.8% (40/130) with endotracheal carbapenemase-producing Acinetobacter spp.; and 14.3% (52/364) with nasal methicillin-resistant S. aureus. The incidence rate of ICU patients becoming colonized with AROs was 9.8 (223/2,276) per 100 patient days. Significant risk factor for AROs colonization was the Charlson Comorbidity Index score. The proportion of ICU patients with HAIs was 23.4% (85/364), and the incidence rate of ICU patients contracting HAIs was 2.3 (85/3,701) per 100 patient days. The vascular catheterization (central venous, arterial and hemofiltration catheter) was significantly associated with hospital-acquired bloodstream infection. Of the 77 patients who developed ICU-acquired infections with one of the five specified bacteria, 44 (57.1%) had prior colonization with the same organism. Vietnamese ICU patients have a high colonization rate with AROs and a high risk of subsequent infections. Future research should focus on monitoring colonization and the development of preventive measures that may halt spread of AROs in ICU settings.

Preterm infant gut microbial patterns related to the development of necrotizing enterocolitis

Objectives: To define gut microbial patterns in preterm infants with and without necrotizing enterocolitis (NEC) and to characterize clinical factors related to the composition of the preterm intestinal microbiome.Methods: Fecal samples were collected at one-week intervals from infants with gestational ages <30 weeks at a single level IV neonatal intensive care unit. Using 16S rRNA gene sequencing, the composition and diversity of microbiota were determined in samples collected from five NEC infants and five matched controls. Hierarchical linear regression was used to identify clinical factors related to microbial diversity and specific bacterial signatures.Results: Low levels of diversity were demonstrated in samples obtained from all preterm infants and antibiotic exposure further decreased diversity among both NEC cases and controls. Fecal microbial composition differed between NEC cases and controls, with a greater abundance of Proteobacteria and bacteria belonging to the class Gammaproteobacteria among NEC infants. Control infants demonstrated a greater abundance of bacteria belonging to the phylum Firmicutes.Conclusion: These findings indicate that an association exists between intestinal Proteobacteria and NEC, and strengthens the notion that an overly exuberant response to Gram-negative products, particularly lipopolysaccharide, in the preterm intestine is involved in NEC pathogenesis. Cumulative exposure to antibiotics corresponded to a reduction in microbial diversity in both NEC cases and controls.

Evaluation of broad-spectrum beta-lactam prescriptions (except carbapenems) in a French teaching hospital

OBJECTIVES

We aimed to assess broad-spectrum beta-lactam prescriptions (except carbapenems) in a French teaching hospital and the impact of controlled dispensing, antimicrobial management team, and antibiotic treatment reassessment on Day 2-3.

PATIENTS AND METHODS

We performed a point-prevalence study in all hospital units and analyzed curative antibiotic broad-spectrum beta-lactam prescriptions. The assessment focused on indication, dosing, combinations, revaluation on Day 2-3, and treatment duration.

RESULTS

Sixty-seven broad-spectrum beta-lactam prescriptions were identified. The main prescriptions were amoxicillin-clavulanic acid (37%, n=25), ceftriaxone (36%, n=24), and piperacillin-tazobactam (16%, n=11). Indications, doses, combinations, and reassessment on Day 2-3 were appropriate, respectively 90% (n=60), 96% (n=64), 94% (33/35 combinations), and 88% (n=59). However, appropriate treatment durations amounted to only 63% (n=42). The benefit of controlled dispensing was observed in terms of overall antibiotic treatment duration: 86% versus 51% adequacy for uncontrolled dispensing of beta-lactams (P=0.02). The antimicrobial management team improved the antibiotic treatment duration: 73% of appropriate durations versus 44% for beta-lactams not monitored by the team, but this difference was not significant.

CONCLUSION

Broad-spectrum beta-lactams were usually well prescribed but the adequacy of treatment duration could be improved, especially by reinforcing the monitoring of prescriptions.

Pathogen colonization of the gastrointestinal microbiome at intensive care unit admission and risk for subsequent death or infection

PURPOSE

Loss of colonization resistance within the gastrointestinal microbiome facilitates the expansion of pathogens and has been associated with death and infection in select populations. We tested whether gut microbiome features at the time of intensive care unit (ICU) admission predict death or infection.

METHODS

This was a prospective cohort study of medical ICU adults. Rectal surveillance swabs were performed at admission, selectively cultured for vancomycin-resistant Enterococcus (VRE), and assessed using 16S rRNA gene sequencing. Patients were followed for 30 days for death or culture-proven bacterial infection.

RESULTS

Of 301 patients, 123 (41%) developed culture-proven infections and 76 (25%) died. Fecal biodiversity (Shannon index) did not differ based on death or infection (p = 0.49). The presence of specific pathogens at ICU admission was associated with subsequent infection with the same organism for Escherichia coli, Pseudomonas spp., Klebsiella spp., and Clostridium difficile, and VRE at admission was associated with subsequent Enterococcus infection. In a multivariable model adjusting for severity of illness, VRE colonization and Enterococcus domination (≥ 30% 16S reads) were both associated with death or all-cause infection (aHR 1.46, 95% CI 1.06-2.00 and aHR 1.47, 95% CI 1.00-2.19, respectively); among patients without VRE colonization, Enterococcus domination was associated with excess risk of death or infection (aHR 2.13, 95% CI 1.06-4.29).

CONCLUSIONS

Enterococcus status at ICU admission was associated with risk for death or all-cause infection, and rectal carriage of common ICU pathogens predicted specific infections. The gastrointestinal microbiome may have a role in risk stratification and early diagnosis of ICU infections.

Potential Adverse Effects of Broad-Spectrum Antimicrobial Exposure in the Intensive Care Unit

Background

The potential adverse effects of empiric broad-spectrum antimicrobial use among patients with suspected but subsequently excluded infection have not been fully characterized. We sought novel methods to quantify the risk of adverse effects of broad-spectrum antimicrobial exposure among patients admitted to an intensive care unit (ICU).

Methods

Among all adult patients admitted to ICUs at a single institution, we selected patients with negative blood cultures who also received ≥1 broad-spectrum antimicrobials. Broad-spectrum antimicrobials were categorized in ≥1 of 5 categories based on their spectrum of activity against potential pathogens. We performed, in serial, 5 cohort studies to measure the effect of each broad-spectrum category on patient outcomes. Exposed patients were defined as those receiving a specific category of broad-spectrum antimicrobial; nonexposed were all other patients in the cohort. The primary outcome was 30-day mortality. Secondary outcomes included length of hospital and ICU stay and nosocomial acquisition of antimicrobial-resistant bacteria (ARB) or Clostridium difficile within 30 days of admission.

Results

Among the study cohort of 1918 patients, 316 (16.5%) died within 30 days, 821 (42.8%) had either a length of hospital stay >7 days or an ICU length of stay >3 days, and 106 (5.5%) acquired either a nosocomial ARB or C. difficile. The short-term use of broad-spectrum antimicrobials in any of the defined broad-spectrum categories was not significantly associated with either primary or secondary outcomes.

Conclusions

The prompt and brief empiric use of defined categories of broad-spectrum antimicrobials could not be associated with additional patient harm.

Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance?

The global spread of antibiotic-resistant pathogens threatens to increase the mortality of cancer patients significantly. We propose that chemotherapy contributes to the emergence of antibiotic-resistant bacteria within the gut and, in combination with antibiotics, drives pathogen overgrowth and translocation into the bloodstream. In our model, these processes are mediated by the effects of chemotherapy on bacterial mutagenesis and horizontal gene transfer, the disruption of commensal gut microbiology, and alterations to host physiology. Clinically, this model manifests as a cycle of recurrent sepsis, with each episode involving ever more resistant organisms and requiring increasingly broad-spectrum antimicrobial therapy. Therapies that restore the gut microbiota following chemotherapy or antibiotics could provide a means to break this cycle of infection and treatment failure.

Piperacillin-tazobactam as alternative to carbapenems for ICU patients

Several studies suggest that alternatives to carbapenems, and particulary beta-lactam/beta-lactamase inhibitor combinations, can be used for therapy of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE)-related infections in non-ICU patients. Little is known concerning ICU patients in whom achieving the desired plasmatic pharmacokinetic/pharmacodynamic (PK/PD) target may be difficult. Also, in vitro susceptibility to beta-lactamase inhibitors might not translate into clinical efficacy. We reviewed the recent clinical studies examining the use of BL/BLI as alternatives to carbapenems for therapy of bloodstream infection, PK/PD data and discuss potential ecological benefit from avoiding the use of carbapenems. With the lack of prospective randomized studies, treating ICU patients with ESBL-PE-related infections using piperacillin-tazobactam should be done with caution. Current data suggest that BL/BLI empirical use should be avoided for therapy of ESBL-PE-related infection. Also, definitive therapy should be reserved to patients in clinical stable condition, after microbial documentation and results of susceptibility tests. Optimization of administration and higher dosage should be used in order to reach pharmacological targets.

Amplification of Antimicrobial Resistance in Gut Flora of Patients Treated with Ceftriaxone

Although antibacterial therapy has an impact on human intestinal flora and the emergence of resistant bacteria, its role in the amplification of antimicrobial resistance and the quantitative exposure-effect relationship is not clear. An observational prospective study was conducted to determine whether and how ceftriaxone exposure is related to amplification of resistance in non-intensive care unit (non-ICU) patients. Serial stool samples from 122 extended-spectrum β-lactamase-positive (ESBL⁺) hospitalized patients were analyzed by quantitative real-time PCR to quantify the resistant gene bla_CTX-M Drug exposure was calculated for each patient by using a population pharmacokinetic model. Multi- and univariate regression and classification regression tree (CART) analyses were used to explore relationships between measures of exposure and amplification of bla_CTX-M genes. Amplification of bla_CTX-M was observed in 0% (0/11) of patients with no treatment and 33% (20/61) of patients treated with ceftriaxone. Stepwise regression analysis showed a significant association between amplification of bla_CTX-M and the plasma area under the concentration-time curve from 0 to 24 h for the unbound fraction of the drug (fAUC_0-24), the maximum concentration of drug in serum for the unbound fraction of the drug (fC_max), and the duration of ceftriaxone therapy. Using CART analysis, amplification of bla_CTX-M was observed in 11/16 (69%) patients treated for >14 days and in 9/40 (23%) patients treated for ≤14 days (P = 0.0019). In the latter group, amplification was observed in 5/7 (71%) patients with an fAUC_0-24 of ≥222 mg · h/liter and in 4/33 (12%) patients with lower drug exposures (P = 0.0033). A similar association was found for an fC_max of ≥30 mg/liter (63% versus 13%, P = 0.0079). A significant association was found between the amplification of bla_CTX-M resistance genes and exposure to ceftriaxone. Both duration of treatment and degree of ceftriaxone exposure have a significant impact on the amplification of resistance genes. (The project described in this paper has been registered at ClinicalTrials.gov under identifier NCT01208519.).

Transmission of Resistant Gram-Negative Bacteria to Health Care Worker Gowns and Gloves during Care of Nursing Home Residents in Veterans Affairs Community Living Centers

The objectives of the study were to estimate the risk of transmission of antibiotic-resistant Gram-negative bacteria (RGNB) to gowns and gloves (G&G) worn by health care workers (HCWs) when providing care to nursing home residents and to identify the types of care and resident characteristics associated with transmission. A multicenter, prospective observational study was conducted with residents and HCWs from Veterans Affairs (VA) nursing homes. Perianal swabs to detect RGNB were collected from residents. HCWs wore G&G during usual care activities, and the G&G were swabbed at the end of the interaction in a standardized manner. Transmission of RGNB from a colonized resident to G&G by type of care was measured. Odds ratios (ORs) associated with type of care or resident characteristics were estimated. Fifty-seven (31%) of 185 enrolled residents were colonized with ≥1 RGNB. RGNB transmission to HCW gloves or gowns occurred during 9% of the interactions (n = 905): 7% to only gloves and 2% to only gowns. Bathing the resident and providing hygiene and toilet assistance were associated with a high risk of transmission. Glucose monitoring and assistance with feeding or medication were associated with a low risk of transmission. In addition, antibiotic use by the resident was strongly associated with greater transmission (OR, 2.51; P < 0.01). RGNB were transferred to HCWs during ∼9% of visits. High-risk types of care were identified for which use of G&G may be prioritized. Antibiotic use was associated with 2.5 times greater risk of transmission, emphasizing the importance of antibiotic stewardship. (This study has been registered at ClinicalTrials.gov under registration no. NCT01350479.).

The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field

The field of infectious disease is undergoing a paradigm shift as the intestinal microbiome is becoming understood. The aim of this review is to inform infectious disease physicians of the potential relevance of the intestinal microbiome to their practice. We searched Medline using both index and text words relating to infectious diseases, microbiome, and probiotics. Relevant articles published up through 2017 were reviewed within Rayyan. The review illustrates pathophysiologic concepts linking the microbiome and infectious diseases; specifically, the intestinal microbiome’s relevance to early immune development, the microbiome and enteric infections, the microbiome’s relevance in compromised hosts, and antimicrobial resistance. Within each subject, there are specific examples of diseases and at-risk patient populations where a role for the microbiome has been strongly established. This provides an overview of the significance of the intestinal microbiome to microbiology, pediatric and adult infectious diseases with an underpinning of concepts useful for the practicing clinician.

The ecology of extended-spectrum β-lactamases (ESBLs) in the developed world

BACKGROUND

Since the initial appearance in the 1980s, Enterobacteriaceae producing extended-spectrum β-lactamase (ESBL) have increased in prevalence and emerged as a major antimicrobial-resistant pathogen. The source of these antimicrobial-resistant bacteria in the developed world is an area of active investigation.

METHODS

A standard internet search was conducted with a focus on the epidemiology and potential sources of ESBL-producing Enterobacteriaceae in the developed world.

RESULTS

The last decade has witnessed several major changes in the epidemiology of these bacteria: replacement of TEM and SHV-type ESBLs by CTX-M-family ESBLs, emergence of Escherichia coli ST131 as a prevalent vehicle of ESBL, and spread of ESBL-producing E. coli in the community. The most studied potential sources of ESBL-producing Enterobacteriaceae in humans in the community include food and companion animals, the environment and person-to-person transmission, though definitive links are yet to be established. Evidence is emerging that international travel may serve as a major source of introduction of ESBL-producing Enterobacteriaceae into the developed world.

CONCLUSIONS

ESBL-producing Enterobacteriaceae has become a major multidrug-resistant pathogen in the last two decades, especially in the community settings. The multifactorial nature of its expansion poses a major challenge in the efforts to control them.

Carbapenem MICs in Escherichia coli and Klebsiella Species Producing Extended-Spectrum β-Lactamases in Critical Care Patients from 2001 to 2009

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae strains are increasing in prevalence worldwide. Carbapenem antibiotics are used as a first line of therapy against ESBL-producing Enterobacteriaceae We examined a cohort of critical care patients for gastrointestinal colonization with carbapenem-resistant ESBL-producing strains (CR-ESBL strains). We cultured samples from this cohort of patients for ESBL-producing Klebsiella spp. and Escherichia coli and then tested the first isolate from each patient for susceptibility to imipenem, doripenem, meropenem, and ertapenem. Multilocus sequence typing was performed on isolates that produced an ESBL and that were carbapenem resistant. Among all patients admitted to an intensive care unit (ICU), 4% were positive for an ESBL-producing isolate and 0.64% were positive for a CR-ESBL strain on surveillance culture. Among the first ESBL-producing E. coli and Klebsiella isolates from the patients' surveillance cultures, 11.2% were carbapenem resistant. Sequence type 14 (ST14), ST15, ST42, and ST258 were the dominant sequence types detected in this cohort of patients, with ST15 and ST258 steadily increasing in prevalence from 2006 to 2009. Patients colonized by a CR-ESBL strain were significantly more likely to receive antipseudomonal and anti-methicillin-resistant Staphylococcus aureus (anti-MRSA) therapy prior to ICU admission than patients colonized by carbapenem-susceptible ESBL-producing strains. They were also significantly more likely to have received a cephalosporin or a carbapenem antibiotic than patients colonized by carbapenem-susceptible ESBL-producing strains. In conclusion, in a cohort of patients residing in intensive care units within the United States, we found that 10% of the isolates were resistant to at least one carbapenem antibiotic. The continued emergence of carbapenem-resistant ESBL-producing strains is of significant concern, as infections due to these organisms are notoriously difficult to treat.

Epidemiology and characteristics of Escherichia coli sequence type 131 (ST131) from long-term care facility residents colonized intestinally with fluoroquinolone-resistant Escherichia coli

The objective of this study was to evaluate molecular and epidemiologic factors associated with Escherichia coli sequence type 131 (ST131) among long-term care facility (LTCF) residents who acquired gastrointestinal tract colonization with fluoroquinolone-resistant E. coli (FQREC). Colonizing isolates from 37 residents who newly developed FQREC colonization at three LTCFs from 2006 to 2008 were evaluated. Twenty-nine (78%) of 37 total FQREC colonizing isolates were ST131. Most ST131 isolates had a distinctive combination of gyrA and parC replacement mutations. The ST131 and non-ST131 isolates differed significantly for the prevalence of many individual virulence factors but not for the proportion that qualified molecularly as extraintestinal pathogenic E. coli (ExPEC) or aggregate virulence factor scores. E. coli ST131 was highly prevalent among LTCF residents with FQREC colonization. Future studies should determine the risk factors for infection among ST131-colonized residents, and assess the potential for increased transmissibility of ST131 in the long-term care setting.

Pathogenic features of heterotrophic plate count bacteria from drinking-water boreholes

Evidence suggests that heterotrophic plate count (HPC) bacteria may be hazardous to humans with weakened health. We investigated the pathogenic potential of HPC bacteria from untreated borehole water, consumed by humans, for: their haemolytic properties, the production of extracellular enzymes such as DNase, proteinase, lipase, lecithinase, hyaluronidase and chondroitinase, the effect simulated gastric fluid has on their survival, as well as the bacteria's antibiotic-susceptible profile. HuTu-80 cells acted as model for the human intestine and were exposed to the HPC isolates to determine their effects on the viability of the cells. Several HPC isolates were α- or β-haemolytic, produced two or more extracellular enzymes, survived the SGF treatment, and showed resistance against selected antibiotics. The isolates were also harmful to the human intestinal cells to varying degrees. A novel pathogen score was calculated for each isolate. Bacillus cereus had the highest pathogen index: the pathogenicity of the other bacteria declined as follows: Aeromonas taiwanensis > Aeromonas hydrophila > Bacillus thuringiensis > Alcaligenes faecalis > Pseudomonas sp. > Bacillus pumilus > Brevibacillus sp. > Bacillus subtilis > Bacillus sp. These results demonstrated that the prevailing standards for HPCs in drinking water may expose humans with compromised immune systems to undue risk.

Genome sequence of OXA-23 producing Acinetobacter baumannii IHIT7853, a carbapenem-resistant strain from a cat belonging to international clone IC1

Background

Multidrug resistance in Acinetobacter baumannii has dramatically increased in recent years worldwide. Thus, last-line antibiotics like carbapenems are increasingly being used which in turn further augments selection pressure for resistant strains. Resistance to carbapenems in A. baumannii is frequently mediated by carbapenemases, particularly OXA-23 and OXA-58. Carbapenemase-producing bacteria are mainly described in human patients and the intestinal tract represents a common source for such pathogens. In this study, we sequenced and analyzed the genome of A. baumannii IHIT7853, a carbapenem-resistant, OXA-23 producing strain isolated from cystitis in a cat in 2000 in Germany.

Results

Phylogenetic analysis revealed that IHIT7853 belonged to the globally distributed international clone IC1 and MLST type ST1/ST231 (Pasteur/Oxford MLST scheme). A phylogenetic tree based on the maximum common genome of 18 A. baumannii isolates placed IHIT7853 close to human clinical isolates, such as the multidrug-resistant (MDR) outbreak strain AYE that was isolated from a patient with pneumonia and cystitis in 2001 in France. The OXA-23 plasmid sequence could be determined as 53,995 bp in size, possessing resistance genes strA and strB in addition to bla_OXA-23.

Conclusions

The analysis of the genome of IHIT7853 reveals that companion animals carry MDR A. baumannii that resemble relevant clonal lineages involved in severe infections in humans. As urinary tract infections are often caused by bacteria that reside in the intestinal tract, future studies should unveil, if the animal gut serves as a source for MDR A. baumannii.

Antimicrobial susceptibility profiles of Escherichia coli and Klebsiella pneumoniae isolated from outpatients in urban and rural districts of Uganda

Background

Antimicrobial resistance is a global public health concern contributing to increased morbidity and mortality particularly in low-income countries. Studies on commensal bacteria are important as they reflect the state of antimicrobial susceptibility patterns in populations. However, susceptibility data on potentially pathogenic commensal bacteria from individuals in communities are still limited. The aim of this cross-sectional study was to determine the susceptibility profiles of Escherichia coli and Klebsiella species isolated from clients attending outpatient clinics in Kampala (urban district) and two rural districts of Uganda, Kayunga and Mpigi. Factors associated with such carriage are also reported.

Results

A total of 1448 participants were recruited into the study with 985 yielding organisms of interest from stool or urine samples (one per client). Most growth occurred from stool samples (636/985, 87 %), of which 620/636 (97 %) grew E. coli while 16 (3 %) were Klebsiella pneumoniae. Growth from urine was 349/985 (35 %) of which 310/349 (89 %) were E. coli while 39 (11 %) K. pneumoniae. High rates of antimicrobial resistance were detected among E. coli and Klebsiella isolates combined: sulphamethoxazole/trimethoprim 70 %, amoxicillin/clavulanate 36 %, chloramphenicol 20 %, ciprofloxacin 11 %, gentamicin 11 %, nitrofurantoin 4 %, ceftriaxone 3 %, piperacillin/tazobactam 27 %, cefoxitin 22 %, and cefepime 15 %. Multidrug resistance was noted in 33 % of the isolates. None of the isolates were resistant to imipenem. Overall, isolates from Kampala were more resistant to antimicrobials. Across the three districts combined, isolates producing beta-lactamase enzymes extended spectrum β-lactamase-(ESBL) and AmpC comprised 5.3 and 13.2 %, respectively. Further, medical procedures involving inoculation were independent risk factors [aOR 50.76 (1.80, 1432.90)] while residing in a rural district and use of sulphamethoxazole/trimethoprim 3 months prior to visiting the outpatient clinics were protective against carriage of multidrug resistant isolates. Furthermore, use of gentamicin was protective against AmpC producing isolates while clients attending HIV/AIDs clinics were less likely to carry such isolates. No factor was independently associated with carriage of ESBL-producing isolates.

Conclusion

Antimicrobial resistance is prevalent among E. coli and K.pneumoniae carried in the gut of clients attending outpatient clinics in Kampala and two rural districts in Uganda. This could complicate treatment options for community-acquired infections caused by the Enterobacteriaceae.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-016-2049-8) contains supplementary material, which is available to authorized users.

Antimicrobials: a global alliance for optimizing their rational use in intra-abdominal infections (AGORA)

Intra-abdominal infections (IAI) are an important cause of morbidity and are frequently associated with poor prognosis, particularly in high-risk patients. The cornerstones in the management of complicated IAIs are timely effective source control with appropriate antimicrobial therapy. Empiric antimicrobial therapy is important in the management of intra-abdominal infections and must be broad enough to cover all likely organisms because inappropriate initial antimicrobial therapy is associated with poor patient outcomes and the development of bacterial resistance. The overuse of antimicrobials is widely accepted as a major driver of some emerging infections (such as C. difficile), the selection of resistant pathogens in individual patients, and for the continued development of antimicrobial resistance globally. The growing emergence of multi-drug resistant organisms and the limited development of new agents available to counteract them have caused an impending crisis with alarming implications, especially with regards to Gram-negative bacteria. An international task force from 79 different countries has joined this project by sharing a document on the rational use of antimicrobials for patients with IAIs. The project has been termed AGORA (Antimicrobials: A Global Alliance for Optimizing their Rational Use in Intra-Abdominal Infections). The authors hope that AGORA, involving many of the world's leading experts, can actively raise awareness in health workers and can improve prescribing behavior in treating IAIs.

Carriage of Enterobacteria Producing Extended-Spectrum β-Lactamases and Composition of the Gut Microbiota in an Amerindian Community

Epidemiological and individual risk factors for colonization by enterobacteria producing extended-spectrum beta-lactamases (E-ESBL) have been studied extensively, but whether such colonization is associated with significant changes in the composition of the rest of the microbiota is still unknown. To address this issue, we assessed in an isolated Amerindian Guianese community whether intestinal carriage of E-ESBL was associated with specificities in gut microbiota using metagenomic and metatranscriptomic approaches. While the richness of taxa of the active microbiota of carriers was similar to that of noncarriers, the taxa were less homogeneous. In addition, species of four genera, Desulfovibrio, Oscillospira, Parabacteroides, and Coprococcus, were significantly more abundant in the active microbiota of noncarriers than in the active microbiota of carriers, whereas such was the case only for species of Desulfovibrio and Oscillospira in the total microbiota. Differential genera in noncarrier microbiota could either be associated with resistance to colonization or be the consequence of the colonization by E-ESBL.

Colonization Resistance of the Gut Microbiota against Clostridium difficile

Antibiotics strongly disrupt the human gut microbiota, which in consequence loses its colonization resistance capacity, allowing infection by opportunistic pathogens such as Clostridium difficile. This bacterium is the main cause of antibiotic-associated diarrhea and a current problem in developed countries, since its incidence and severity have increased during the last years. Furthermore, the emergence of antibiotic resistance strains has reduced the efficiency of the standard treatment with antibiotics, leading to a higher rate of relapses. Here, we review recent efforts focused on the impact of antibiotics in the gut microbiome and their relationship with C. difficile colonization, as well as, in the identification of bacteria and mechanisms involved in the protection against C. difficile infection. Since a healthy gut microbiota is able to avoid pathogen colonization, restoration of the gut microbiota seems to be the most promising approach to face C. difficile infection, especially for recurrent cases. Therefore, it would be possible to design probiotics for patients undergoing antimicrobial therapies in order to prevent or fight the expansion of the pathogen in the gut ecosystem.

Characterising the Transmission Dynamics of Acinetobacter baumannii in Intensive Care Units Using Hidden Markov Models

Little is known about the transmission dynamics of Acinetobacter baumannii in hospitals, despite such information being critical for designing effective infection control measures. In the absence of comprehensive epidemiological data, mathematical modelling is an attractive approach to understanding transmission process. The statistical challenge in estimating transmission parameters from infection data arises from the fact that most patients are colonised asymptomatically and therefore the transmission process is not fully observed. Hidden Markov models (HMMs) can overcome this problem. We developed a continuous-time structured HMM to characterise the transmission dynamics, and to quantify the relative importance of different acquisition sources of A. baumannii in intensive care units (ICUs) in three hospitals in Melbourne, Australia. The hidden states were the total number of patients colonised with A. baumannii (both detected and undetected). The model input was monthly incidence data of the number of detected colonised patients (observations). A Bayesian framework with Markov chain Monte Carlo algorithm was used for parameter estimations. We estimated that 96-98% of acquisition in Hospital 1 and 3 was due to cross-transmission between patients; whereas most colonisation in Hospital 2 was due to other sources (sporadic acquisition). On average, it takes 20 and 31 days for each susceptible individual in Hospital 1 and Hospital 3 to become colonised as a result of cross-transmission, respectively; whereas it takes 17 days to observe one new colonisation from sporadic acquisition in Hospital 2. The basic reproduction ratio (R0) for Hospital 1, 2 and 3 was 1.5, 0.02 and 1.6, respectively. Our study is the first to characterise the transmission dynamics of A. baumannii using mathematical modelling. We showed that HMMs can be applied to sparse hospital infection data to estimate transmission parameters despite unobserved events and imperfect detection of the organism. Our results highlight the need to optimise infection control in ICUs.