Prevalent phenotypes and antibiotic resistance in Escherichia coli and Klebsiella pneumoniae at an Indian tertiary care hospital: plasmid-mediated cefoxitin resistance

Diversity and Distribution of β-Lactamase Genes Circulating in Indian Isolates of Multidrug-Resistant Klebsiella pneumoniae

Klebsiella pneumoniae (Kp) has gained prominence in the last two decades due to its global spread as a multidrug-resistant (MDR) pathogen. Further, carbapenem-resistant Kp are emerging at an alarming rate. The objective of this study was (1) to evaluate the prevalence of β-lactamases, especially carbapenemases, in Kp isolates from India, and (2) determine the most prevalent sequence type (ST) and plasmids, and their association with β-lactamases. Clinical samples of K. pneumoniae (n = 65) were collected from various pathology labs, and drug susceptibility and minimum inhibitory concentrations (MIC) were detected. Whole genome sequencing (WGS) was performed for n = 22 resistant isolates, including multidrug-resistant (MDR) (n = 4), extensively drug-resistant (XDR) (n = 15), and pandrug-resistant (PDR) (n = 3) categories, and genomic analysis was performed using various bioinformatics tools. Additional Indian MDRKp genomes (n = 187) were retrieved using the Pathosystems Resource Integration Center (PATRIC) database. Detection of β-lactamase genes, location (on chromosome or plasmid), plasmid replicons, and ST of genomes was carried out using CARD, mlplasmids, PlasmidFinder, and PubMLST, respectively. All data were analyzed and summarized using the iTOL tool. ST231 was highest, followed by ST147, ST2096, and ST14, among Indian isolates. bla_ampH was detected as the most prevalent gene, followed by bla_CTX-M-15 and bla_TEM-1. Among carbapenemase genes, bla_OXA-232 was prevalent and associated with ST231, ST2096, and ST14, which was followed by bla_NDM-5, which was observed to be prevalent in ST147, ST395, and ST437. ST231 genomes were most commonly found to carry Col440I and ColKP3 plasmids. ST16 carried mainly ColKP3, and Col(BS512) was abundantly present in ST147 genomes. One Kp isolate with a novel MLST profile was identified, which carried bla_CTX-M-15, bla_OXA-1, and bla_TEM-1. ST16 and ST14 are mostly dual-producers of carbapenem and ESBL genes and could be emerging high-risk clones in India.

Drug utilization, rationality, and cost analysis of antimicrobial medicines in a tertiary care teaching hospital of Northern India: A prospective, observational study

BACKGROUND:

The burden of bacterial infections is huge and grossly under-represented in the current health-care system. Inappropriate use of antimicrobial medicines (AMMs) poses a potential hazard to patients by causing antibiotic resistance. This study was conducted to assess the: (i) AMM consumption and use patterns in patients attending the outpatients and inpatients of Medicine and Surgery departments of the hospital. (ii) Appropriateness of the AMM in the treatment prescribed, and (iii) cost incurred on their use in admitted patients.

MATERIALS AND METHODS:

An observational, prospective study was conducted among inpatients and outpatients of the Medicine and Surgery departments of a tertiary care hospital of northern India. Analysis of 2128 prescriptions and 200 inpatient records was performed using a predesigned format. The use of AMMs was reviewed using anatomical therapeutic chemical classification and defined daily doses (DDDs). To evaluate the expenditure incurred on AMMs, ABC analysis was performed.

RESULTS:

AMMs were prescribed to 37.9% outpatients and 73% of admitted patients. The percentage encounters with AMMs was 40.6% (medicine) and 25.6% (surgery) outpatients. The total DDDs/100 patient days of AMMs in medicine and surgery were 3369 and 2247. Bacteriological evidence of infection and AMM sensitivity was present in only 8.5% of cases. Over 90% of AMMs were prescribed from the hospital essential medicines list. Most of the AMMs were administered parenterally (64.9%). Multiple AMMs were prescribed more to inpatients (84.2% vs. 4.2% outpatients). Overall, expenditure on AMM was 33% of the total cost of treatment on medicine. ABC analysis showed that 74% of the expenditure was due to newer, expensive AMM, which constituted only 9% of the AMM used. The AMM therapy was found to be appropriate in 88% of cases as per Kunin's criteria for rationality.

CONCLUSION:

AMMs are being commonly prescribed without confirmation of AMM sensitivity in the hospital. A large proportion of expenditure is being incurred on expensive AMM used in a few number of patients. There is a need for developing a policy for rational use of AMM in the health facility.

The first report of Enterobacter gergoviae carrying bla NDM-1 in Iran

OBJECTIVES

Prompt detection of extended-spectrum β-lactamases (ESBL) and carbapenemase-producing enterobacteriaceae is crucial for infection prevention and control strategies. The present study aimed to characterize the ESBL and carbapenemase genes among Enterobacter isolates from an Iranian inpatient population.

MATERIALS AND METHODS

A total of 96 Enterobacter isolates obtained from inpatients between June 2016 and March 2017, were identified by the conventional microbiological methods and diagnostic kits. Antimicrobial susceptibility pattern was performed using the disk diffusion method. The ESBL and carbapenemase genes were screened using polymerase chain reaction (PCR).

RESULTS

All clinical isolates of Enterobacter were classified as E. gergoviae (52, 54.2%), E. aerogenes (34, 35.4%), E. cloacae (7, 7.3%), Cronobacter (E). sakazakii (3, 3.1%). The highest and lowest antimicrobial resistance rates were observed against ampicillin (93.8%) and imipenem (21.9%). High prevalence of multi-drug resistance (MDR=96.9%) was substantial. Of the 96 Enterobacter isolates, 35 (36.5%) and 28 (29.2%) were phenotypically ESBL-positive and non-susceptible carbapenem, respectively. Overall, the frequency of evaluated genes was as follows: blaCTX-M =25 (26%), blaTEM =30 (31.3%), blaSHV =12 (12.5%), blaIMP =3 (3.1%), blaVIM =0 (0%), blaNDM =8 (8.3%), and blaKPC =0 (0%).

CONCLUSION

In this study, we report for the first time the presence of E. gergoviae harboring blaNDM from an Iranian population. Regarding the increase of MDR Enterobacter spp. in our region, strict hygiene rules will be needed to control the quick spread of ESBL and carbapenemase-producing Enterobacter isolates in healthcare facilities of developing countries.

Isolation of Multidrug-Resistant Escherichia coli O157 from Goats in the Somali Region of Ethiopia: A Cross-Sectional, Abattoir-Based Study

Toxigenic Escherichia coli (E. coli) are an important cause of gastroenteritis in developing countries. In Ethiopia, gastroenteritis due to food-borne disease is a leading cause of death. Yet, there is no surveillance for E. coli O157 and little is known about the carriage of this pathogen in Ethiopia's livestock. This study aimed to assess the prevalence and levels of antimicrobial resistance of E. coli O157 in goat meat, feces, and environmental samples collected at a large abattoir in the Somali region of Ethiopia. The samples were enriched in modified tryptone broth containing novobiocin, and plated onto sorbitol MacConkey agar. Isolates were confirmed using indole test and latex agglutination. Antimicrobial susceptibility testing was conducted using the disk diffusion method. A total of 235 samples, including 93 goat carcass swabs, 93 cecal contents, 14 water, 20 hand, and 15 knife swabs were collected. Overall, six (2.5%) samples were contaminated with E. coli O157 of which two (2.1%) were isolated from cecal contents, three (3.2%) from carcass swabs, and one (7.1%) from water. All isolates were resistant to at least two of the 18 antimicrobials tested. Two isolates (33.3%) were resistant to more than five antimicrobials. Abattoir facilities and slaughter techniques were conducive to carcass contamination. This study highlights how poor hygiene and slaughter practice can result in contaminated meat, which is especially risky in Ethiopia because of the common practice of eating raw meat. We detect multi-resistance to drugs not used in goats, suggesting that drugs used to treat human infections may be the originators of antimicrobial resistance in livestock in this ecosystem. The isolation of multidrug-resistant E. coli O157 from goats from a remote pastoralist system highlights the need for global action on regulating and monitoring antimicrobial use in both human and animal populations.

Modeling the synergistic antibacterial effects of honey characteristics of different botanical origins from the Sahara Desert of Algeria

Background: Honey has multiple therapeutic properties due to its composition with diverse components.

Objectives: This study aims to investigate the antimicrobial efficacy of Saharan honeys against bacterial pathogens, the variation of honey floral origins, and its physicochemical characteristics.

Materials and Methods: The antimicrobial activity of 32 samples of honey collected from the Algerian Sahara Desert was tested on four bacteria; Bacillus subtilis, Clostridium perfringens, Escherichia coli, and Staphylococcus aureus. The botanical origin of honeys and their physicochemical properties were determined and their combined antibacterial effects were modeled using a generalized linear mixed model (GLMM).

Results: Out of the 32 study samples, 14 were monofloral and 18 were multifloral. The pollen density was on average 7.86 × 10⁶ grains/10 g of honey, water content was 14.6%, electrical conductivity (EC) was 0.5 μS/cm, pH was 4.38 ± 0 50, hydroxymethylfurfural (HMF) content was 82 mg/kg of honey, total sugars = 83%, reducing sugars = 71%, and the concentration of proline = 525.5 ± 550.2 mg/kg of honey. GLMM revealed that the antibacterial effect of honey varied significantly between bacteria and floral origins. This effect increased with increasing of water content and reducing sugars in honey, but it significantly decreased with increase of honey EC. E. coli was the most sensitive species with an inhibition zone of 10.1 ± 4.7 mm, while C. perfringens was the less sensitive. Honeys dominated by pollen of Fabaceae sp. were most effective with an overall antimicrobial activity equals to 13.5 ± 4.7 mm.

Conclusion: Saharan honeys, of certain botanical origins, have physicochemical and pollinic characteristics with relevant potential for antibacterial purposes. This encourages a more comprehensive characterization of honeys with in vivo and in vitro investigations.

Antimicrobial susceptibility pattern of extended-spectrum β-lactamase-producing bacteria causing nosocomial urinary tract infections in an Iranian referral teaching hospital

OBJECTIVE

Gram-negative bacilli are the most important cause of nosocomial urinary tract infections (UTIs). The production of extended-spectrum β-lactamase (ESBL) enzymes is a common mechanism of resistance among these bacteria. The aim of this study was to determine the rate of ESBL producing Gram-negative bacteria causing nosocomial UTI in a referral hospital as well as their susceptibility pattern to the most commonly used antibiotics.

METHODS

In a prospective cross-sectional study performed over a 6-month period, urinary specimens obtained from hospitalized patients with documented culture-proved nosocomial UTI (age range of 1-87 years). Isolated aerobic Gram-negative bacteria underwent further microbiologic tests for detection of ESBL, as well as antimicrobial susceptibility test using Kirby-Bauer (disk diffusion) and E-test methods.

FINDINGS

During the study period, 213 urine samples were detected to have growth of Gram-negative organism. Escherichia coli was the most frequently isolated organism (61%). ESBL was detected in 102 isolates including 38.5% of E. coli, 39.5% of Klebsiella pneumonia, 88.5% of Pseudomonas aeruginosa, and 100% of Acinetobacter baumannii strains. Imipenem and meropenem were the most effective antibiotics on E. coli and K. pneumoniae strains. P. aeruginosa and A. baumannii strains showed high resistance to all tested antibiotics.

CONCLUSION

Large numbers of Gram-negative bacteria causing nosocomial UTIs produce ESBL with most being multidrug-resistant. Therefore, routine ESBL detection testing and subsequent antibiogram with disk diffusion method could be useful to determine the best treatment options for UTI.

The Beta Lactam Antibiotics as an Empirical Therapy in a Developing Country: An Update on Their Current Status and Recommendations to Counter the Resistance against Them

In a developing country like India, where the patients have to bear the cost of their healthcare, the microbiological culture and the sensitivity testing of each and every infection is not feasible. Moreover, there are lacunae in the data storage, management and the sharing of knowledge with respect to the microorganisms which are prevalent in the local geographical area and with respect to the antibiotics which are effective against them. Thus, an empirical therapy for treating infections is imperative in such a setting. The beta lactam antibiotics have been widely used for the empirical treatment of infections since the the discovery of penicillin. Many generations of beta lactams have been launched with, the claims of a higher sensitivity and less resistance, but their sensitivity has drastically decreased over time. Thus, the preference for beta lactams, especially the cephalosporins, as an empirical therapy, among the prescribers was justified initially, but the current sensitivity patterns do not support their empirical use in hospital and community acquired infections. There is a need for increasing the awareness and the attitudinal change among the prescribers, screening of the antibiotic prescriptions, the strict implementation of antibiotic policies in hospital settings, restricting the hospital supplies and avoiding the prescriptions of beta lactams, a regular census of the local sensitivity patterns to formulate and update the antibiotic policies, upgradation of the laboratory facilities for a better and faster detection of the isolates, proper collection, analyses and sharing of the data and the encouragement of the research and development of newer antibiotics with novel mechanisms of action.

Extended-spectrum beta-lactamase-producing Escherichia coli in patients with travellers' diarrhoea

The identification of patients carrying extended-spectrum beta-lactamase (ESBL)-producing bacteria is important, since these patients are at risk of receiving inappropriate empirical therapy if they become infected. The purpose of this study was to investigate the occurrence of ESBL-producing bacteria in patients with travellers' diarrhoea. Patients with travellers' diarrhoea (N = 242) having delivered stool samples for the diagnosis of Salmonella, Shigella, Yersinia or Campylobacter, were also examined for ESBL-producing Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis. The overall prevalence of faecal carriage of ESBL-producing bacteria was 24% (58/242). Of the patients who had travelled in Europe, 3% (2/63) were found to be ESBL carriers in comparison to 36% (50/138) of those who had travelled outside Europe. ESBL-producing E. coli was especially common among patients returning from India (11/14), Egypt (19/38; 50%) and Thailand (8/38; 22%). In total, 90% of the genes of the ESBL-positive samples were of CTX-M type. The CTX-M-1 group dominated, followed by the CTX-M-9 group. The repetitive sequence-based PCR fingerprint pattern showed that there was no similarity between the ESBL strains found. Patients who have travelled outside Europe are at high risk of being colonized with ESBL-producing Enterobacteriaceae, and, if infected, are also at risk of receiving inappropriate empirical antibiotic therapy.

Citrobacter spp. simultaneously harboring blaCTX-M, blaTEM, blaSHV, blaampC, and insertion sequences IS26 and orf513: an evolutionary phenomenon of recent concern for antibiotic resistance

A collection of 40 confirmed isolates of Citrobacter spp., obtained from the culture of 5,732 clinical samples during 2006 to 2008, was studied for the presence of blaCTX-M, blaTEM, blaSHV, and blaampC by monoplex and multiplex PCRs. These isolates were also looked at for the presence of insertion elements IS26 and orf513, which play an important role in the resistance gene pool. blaCTX-M, blaTEM, blaSHV, and blaampC were noticed in 67.5%, 40%, 25%, and 40% of isolates, respectively. Sequencing for the specific CTX-M type revealed the presence of CTX-M-15-type extended-spectrum beta-lactamases (ESBL). sul1-type integrons were detected in 32.5% (13/40) of isolates, and a single plasmid of ca. approximately 22 kb was also noticed in all the isolates harboring bla genes. A total of 48.2% (13/27) of isolates harboring blaCTX-M alleles were found to carry IS26 elements and 53.4% (7/13) of isolates harboring the sul1-type integrons were found to carry orf513. Alarmingly, a few isolates simultaneously carried IS26 and orf513, reflecting the occurrence of complex evolution. All the Citrobacter isolates were noticed to produce an amplicon of 400 bp in an IS26 PCR, similar to that of the predominant UK CTX-M-15-producing Escherichia coli clone (clone A) and suggesting a probable genetic relatedness between the two, which could not be proved with British and Indian E. coli isolates in our earlier studies. Here, a first report is being presented describing the occurrence of blaCTX-M-15 in Indian Citrobacter spp. This is also the first report describing the simultaneous occurrence of blaTEM, blaSHV, and blaampC along with blaCTX-M in class 1 integrons. The recent findings indicate that the genetic environment of blaCTX-M-15 has changed through the insertion of IS26 and orf513, although the consequences of these events remain uncertain. It perhaps also suggests a "turnover" of these mobile elements in the population over time.

Pharmaco-EcoMicrobiology: a newer component of medical sciences bridging pharmacovigilance, ecology, and environmental microbiology

Environmental scientists are now raising great concern on the impact of drugs on the environment and microbiologists are concerned about increasing antibiotic resistance due to irrational usage. However, a focus on the impact by the use of antibiotics (irrational/prescribed) to the environment at therapeutic doses has not been instituted. Even the World Health Organization (WHO) defined "Pharmacovigilance" activities as the monitoring, detection, assessment, understanding and prevention of any adverse reactions to drugs at therapeutic concentration on animals and humans. Nevertheless, there is little attention being given to identifying the adverse effects (ADEs) of antimicrobial agents on the environment (given at therapeutic doses). This issue has been highlighted in the present commentary and a new domain, "Pharmaco-EcoMicrobiology", has been proposed which should deal with and monitor such adverse effects. The term "Pharmaco-EcoMicrobiology" has been proposed to define the interplay between antimicrobial pharmacological agents and animate microbial ecology. This new domain, "Pharmaco-EcoMicrobiology", has been derived by the aggregation of three important branches of science (pharmacology+ecology+microbiology) and would be responsible for studying the ADEs due to antimicrobial drugs excreted in environment.