Occurrence and characterization of carbapenem-resistant Gram-negative bacilli: A collaborative study of antibiotic-resistant bacteria between Indonesia and Japan

Antibiotic resistances of Pseudomonas aeruginosa and Acinetobacter baumannii in urine cultures: experience in a hospital of Southeast Spain

The objectives of this study were to perform a systematic review of publications between 2010 and 2021 on the antibiotic resistance of Pseudomonas aeruginosa and Acinetobacter baumannii from urinary tract infections and to analyze changes over time in hospital urine cultures from 2016 through 2021. The literature was searched, and a retrospective cross-sectional descriptive study was performed in the hospital. Out of 21 838 positive urine cultures, 3.86% were due to P. aeruginosa and 0.44% were due to A. baumannii. For P. aeruginosa, lower resistance rates were observed to virtually all tested antibiotics than were obtained in the systematic review, and the present series of hospital samples showed an in vitro resistance rate <10% to ceftazidime, cefepime, meropenem, piperacillin-tazobactam, amikacin, tobramycin, and colistin. For A. baumannii, the resistance rates to almost all antibiotics were higher in the present series than in the systematic review, being lowest to colistin (10%). Both microorganisms show reduced in vitro susceptibility to some antibiotics during the years of the COVID-19 pandemic in comparison to previous years. In our setting, both piperacillin-tazobactam and meropenem can be recommended for the empirical treatment of UTIs by P. aeruginosa, whereas only colistin can be recommended for UTIs by A. baumannii.

Emergence of Extended-Spectrum Beta-Lactamase and Carbapenemase Producing Gram Negative Non-Fermenters at Selected Hospitals of Northeast Ethiopia: A Prospective Cross-Sectional Study

Background

The emergence and spread of extended-spectrum β-lactamases (ESβLs) and carbapenemase (CP) producing gram negative non-fermenters are becoming a serious public health threat globally. Infections caused by these pathogens limit treatment options and contribute to the significant morbidity and mortality. Thus, to reduce their spread, early detection of these superbugs is very crucial. This study therefore aimed to assess the prevalence of ESβLs and CP producing gram negative non-fermenters at selected hospitals of North East Ethiopia.

Methods

A cross-sectional study was conducted from January to June 2021. Acinetobacter baumannii (A. baumannii) and Pseudomonas aeruginosa (P. aeruginosa) were identified using standard bacteriological techniques. ESβL and CP production were detected by combined disk diffusion and modified carbapenem inhibitory methods, respectively. Data were collected via face-to-face interview and patient card review. Chi-squared and Fisher's exact tests were calculated and p-value < 0.05 was considered statistically significant.

Results

A total of 384 patients participated in this study. Overall, 30 (7.8%) patients had positive culture for A. baumannii and P. aeruginosa. The prevalence of A. baumannii was 20 (5.2%) and that of P. aeruginosa was 10 (2.6%). From the overall isolates, 16 (53.3%) were ESβL and the proportion of carbapenemase production was 4 (13.3%). ESβL production was 8 (40%) in A. baumannii and 8 (80%) in P. aeruginosa isolates. ESβL production infections were significantly associated with hospitalization (p=0.004). Intravenous catheterization, hospitalization, and surgery had significant association with ESβL production (p<0.005). All isolates of A. baumannii and P. aeruginosa were MDR.

Conclusion

ESβL and carbapenemase production among A. baumannii and P. aeruginosa were high in the selected hospitals. The treatment of such resistant infectious agents should be guided by antimicrobial susceptibility test in a study setting. Thus, restricted and wise use of antibiotics is highly recommended to contain the spread of these superbugs. Hospitals should develop infection prevention guidelines to prevent the spread of resistant pathogens in hospitalized patients.

Magnitude and antimicrobial susceptibility profiles of Gram-Negative bacterial isolates among patients suspected of urinary tract infections in Arba Minch General Hospital, southern Ethiopia

The emergence of drug-resistant Gram-negative bacterial uropathogens poses a grave threat worldwide, howbeit studies on their magnitude are limited in most African countries, including Ethiopia. Therefore, measuring the extent of their drug resistance is essential for developing strategies to confine the spread. A cross-sectional study was conducted at title hospital from 01 June to 31 August 2020. Midstream urine specimens were collected and inoculated onto MacConkey agar. Positive urine cultures showing significant bacteriuria as per the Kass count (>105 CFU/mL) were further subjected to biochemical tests to identify the type of uropathogens. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disk diffusion technique, and potential carbapenemase producers were phenotypically determined by the modified carbapenem inactivation method as per the CLSI guidelines. Data were analyzed using SPSS version 26; P-value <0.05 was considered statistically significant. Totally, 422 patients were included, and the majority were females (54.7%). The prevalence of carbapenem-resistant Gram-negative uropathogens was 12.9%, and 64.7% of them were carbapenemase producers. Klebsiella pneumoniae (n = 5) was the predominant carbapenemase producer, followed by Pseudomonas aeruginosa (n = 4). Consumption of antibiotics prior to six months of commencement of the study, the presence of chronic diseases and hospitalizations were statistically associated with UTI caused by carbapenem-resistant Gram-negative uropathogens. Carbapenemase producers were resistant to most of the antibiotics tested. Our findings highlight the need for periodic regional bacteriological surveillance programs to guide empirical antibiotic therapy of UTI.

Effect of Ciprofloxacin, Levofloxacin, and Ofloxacin on Pseudomonas aeruginosa: A case control study with time kill curve analysis

Background

Antibiotic resistance is closely related to therapy failure. Most antibiotic resistance is caused by delays in determining antibiotic agents, low administration doses, long periods between doses (inadequate pharmacokinetics) and single drug administration in infections caused by more than one pathogen. Treatment of Pseudomonas aeruginosa (P. aeruginosa) with ciprofloxacin, levofloxacin, and ofloxacin as monotherapy can lead to drug resistance, although combination therapy also does not provide a better outcome.

Objective

To analyze the time-kill curve for P. aeruginosa and Multidrug resistance (MDR) P. aeruginosa.

Methods

This research is a case control study using isolates of P. aeruginosa ATCC 27853, clinical isolates of P. aeruginosa and MDR P. aeruginosa. Exposure of ciprofloxacin, levofloxacin, and ofloxacin to isolates with 1MIC, 2MIC, and 4MIC were then cultured at 0, 2, 4, 6, 8, 24 h of testing, then counting the number of colonies that grew and then analyzed by time-kill curve and statistical tests. The statistical test used in this study was the ANOVA and Mann-Whitney test with p < 0.05.

Results

Ciprofloxacin and ofloxacin achieved bactericidal activity, especially at a concentration of 4MIC. Levofloxacin ultimately achieved bactericidal activity at all concentrations. Statistical analysis showed there were significant differences in the number of colonies p < 0.001 in the second, fourth, sixth, and eighth hour between the three isolates, p < 0.001 in the sixth and second 4 h between 1MIC and 4MIC, p = 0.012 in the second 4 h between levofloxacin and ofloxacin antibiotics.

Conclusion

Levofloxacin has shown to have better bactericidal activity than ciprofloxacin, and ciprofloxacin has almost the same bactericidal activity as ofloxacin in vitro tests seen from the time-kill curve.

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Antibiotics for P. aeruginosa were effective in reducing colonies at 8 h.

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A significant comparison for antibiotics on P. aeruginosa and MDR.

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Levofloxacin is the most effective compared to ciprofloxacin and ofloxacin for P. aeruginosa.

Molecular Epidemiology of Clinical Carbapenem-Resistant Acinetobacter baumannii-calcoaceticus complex Isolates in Tertiary Care Hospitals in Java and Sulawesi Islands, Indonesia

Carbapenem-resistant Acinetobacter baumannii (A. baumannii)-calcoaceticus complex (CRAb-cc) is an important pathogen causing nosocomial infections worldwide; however, molecular epidemiology of the A. baumannii-calcoaceticus complex in Indonesian hospitals is scarce. This study aimed to determine the clonal relatedness of CRAb-cc in two tertiary care hospitals in Malang and Manado in Indonesia. The CRAb-cc isolates from routine clinical cultures in two tertiary care hospitals in Malang and Manado were identified using the Vitek2^® system (bioMérieux, Lyon, France). Multi-locus variable-number tandem-repeat analysis (MLVA) typing, multi-locus sequence typing (MLST), clonal complex (CC), and phylogenetic tree analysis were conducted for a subset of isolates. Seventy-three CRAb-cc isolates were collected. The CRAb-cc isolates were frequently found among lower-respiratory-tract specimens. We detected the MLVA type (MT) 1, MT3, and MT4 CRAB-cc isolates belonging to the sequence type (ST) 642, and CC1 was the predominant clone in this study. In conclusion, we identified the clonal relatedness of A. baumannii-calcoaceticus complex isolates in two tertiary care hospitals in Malang and Manado in Indonesia. Further study is required to investigate the clinical importance and distribution of ST642 in Indonesian hospitals for developing prevention and control measures.

The Economic Impact of Carbapenem Resistant-Non Lactose Fermenter and Enterobacteriaceae Infections on Hospital Costs in Dr. Soetomo General Academic Hospital Surabaya, Indonesia

Background: Carbapenem resistant-non lactose fermenter (CR-NLF) and Carbapenem resistant-Enterobacteriaceae (CR-E) bacterial infections are likely to be a global threat to people’s health. However, studies on the economic impacts according to the hospital setting are very scarce. The study aimed to explore the impact of CR-NLF (Acinetobacter baumannii = CRAB) & Pseudomonas aeruginosa = CRPA) and CR-E (Escherichia coli = CREC) & Klebsiella pneumoniae = CRKP) infections on hospital costs from a payer perspective among patients admitted to Dr.Soetomo Hospital, Surabaya, Indonesia. Methods: In the retrospective case-control study, medical records of all included patients hospitalized during 2018−2021 were reviewed for CRAB, CRPA, CREC, CRKP, and carbapenem sensitive (CSAB, CSPA, CSEC, CSKP) were collected. We retrieved the data of age, gender, clinical specimen, dates of admission, and discharge status. The outcomes of interest were hospital length of stay and hospitalization cost. Results: The cost for CR-NLFs infections was higher than carbapenem sensitive, $3026.24 versus $1299.28 (p < 0.05). There was no significant difference between CR-E against carbapenem sensitive. It showed that the highest impact of the cost was CRAB, followed by CRPA, CRKP, and CREC. The bed, antibiotics, pharmacy, and diagnostic costs of CR-NLFIs were significantly higher than CR-E. Conclusion: This study showed that the hospital cost and expenditure of CR-NLFs per patient were higher than CS. The hospital cost per patient for CR-NLF was higher than CR-E.

Excess mortality attributable to antimicrobial-resistant bacterial bloodstream infection at a tertiary-care hospital in Indonesia

The burden of antimicrobial-resistant (AMR) infections in low and middle-income countries (LMICs) is largely unknown. Here, we evaluate attributable mortality of AMR infections in Indonesia. We used routine databases of the microbiology laboratory and hospital admission at Dr. Wahidin Sudirohusodo Hospital, a tertiary-care hospital in South Sulawesi from 2015 to 2018. Of 77,752 hospitalized patients, 8,341 (10.7%) had at least one blood culture taken. Among patients with bacteriologically confirmed bloodstream infections (BSI), the proportions of patients with AMR BSI were 78% (81/104) for third-generation cephalosporin-resistant (3GCR) Escherichia coli, 4% (4/104) for 3GCR plus carbapenem-resistant E. coli, 56% (96/171) for 3GCR Klebsiella pneumoniae, 25% (43/171) for 3GCR plus carbapenem-resistant K. pneumoniae, 51% (124/245) for methicillin-resistant Staphylococcus aureus, 48% (82/171) for carbapenem-resistant Acinetobacter spp., and 19% (13/68) for carbapenem-resistant Pseudomonas aeruginosa. Observed in-hospital mortality of patients with AMR BSI was 49.7% (220/443). Compared with patients with antimicrobial-susceptible BSI and adjusted for potential confounders, the excess mortality attributable to AMR BSI was -0.01 (95% CI: -15.4, 15.4) percentage points. Compared with patients without a BSI with a target pathogen and adjusted for potential confounders, the excess mortality attributable to AMR BSI was 29.7 (95%CI: 26.1, 33.2) percentage points. This suggests that if all the AMR BSI were replaced by no infection, 130 (95%CI: 114, 145) deaths among 443 patients with AMR BSI might have been prevented. In conclusion, the burden of AMR infections in Indonesian hospitals is likely high. Similar large-scale evaluations should be performed across LMICs to inform interventions to mitigate AMR-associated mortality.

Global surveillance of antimicrobial resistance and hypervirulence in Klebsiella pneumoniae from LMICs: An in-silico approach

The global emergence of antimicrobial resistance (AMR) among pathogens is a major public health crisis that might soon lead to a post-antibiotic era. Klebsiella pneumoniae, included in the World Health Organization list of critical priority pathogens, is an emerging threat to global health owing to the rapid rise of convergent AMR and hypervirulent strains. Comprehensive epidemiology of AMR-hypervirulent determinants in K. pneumoniae from Low-and Middle-Income Countries (LMICs) is still lacking. As part of rapid risk assessment, an in-silico approach was employed to characterize the AMR and hypervirulence determinants in K. pneumoniae from LMICs. Genomic data of 2432 K. pneumoniae strains were obtained from 33 LMICs representing 4 continents; Asia (n = 12), Africa (n = 18), N. America (n = 2) and Europe (n = 1). All the analysed strains were multiple-drug resistant and 13.6% of them were hypervirulent as well. The co-existence of antibiotic resistant genes conferring concomitant resistance towards life-saving drugs (carbapenems, colistin, fluoroquinolones and fosfomycin) were also observed among the strains, thereby challenging the efficacy of current treatment strategies. The emergence of convergent strains of K. pneumoniae carrying both multi-drug resistance and hypervirulence-associated genes in 12 LMICs is highlighted in this study. Asian region was identified as the major hotspot for convergent strains, especially being confined to 3 countries (India, Pakistan and Vietnam), further exacerbating the situation. This represents a major challenge to disease treatment and public health management in the LMICs. Regular surveillance for emergence of convergence and necessary interventions in the high-risk regions are strongly recommended.

Burden of illness in US hospitals due to carbapenem-resistant Gram-negative urinary tract infections in patients with or without bacteraemia

Background

Urinary tract infections (UTIs) are the most common infections caused by Gram-negative bacteria and represent a major healthcare burden. Carbapenem-resistant (CR) strains of Enterobacterales and non-lactose fermenting pathogens further complicate treatment approaches.

Methods

We conducted a retrospective analysis of the US Premier Healthcare Database (2014–2019) in hospitalised adults with a UTI to estimate the healthcare burden of Gram-negative CR UTIs among patients with or without concurrent bacteraemia.

Results

Among the 47,496 patients with UTI analysed, CR infections were present in 2076 (4.4%). Bacteraemia was present in 24.5% of all UTI patients, and 1.7% of these were caused by a CR pathogen. The most frequent CR pathogens were Pseudomonas aeruginosa (49.4%) and Klebsiella pneumoniae (14.2%). Patients with CR infections had a significantly longer hospital length of stay (LOS) (median [range] 8 [5–12] days vs 6 [4–10] days, P < 0.001), were less likely to be discharged home (38.4% vs 51.0%, P < 0.001), had a higher readmission rate (22.6% vs 13.5%, P < 0.001), and had greater LOS-associated charges (mean US$ 91,752 vs US$ 66,011, P < 0.001) than patients with carbapenem-susceptible (CS) infections, respectively. The impact of CR pathogens was greater in patients with bacteraemia (or urosepsis) and these CR urosepsis patients had a significantly higher rate of mortality than those with CS urosepsis (10.5% vs 6.0%, P < 0.001).

Conclusions

Among hospitalised patients with UTIs, the presence of a CR organism and bacteraemia increased the burden of disease, with worse outcomes and higher hospitalisation charges than disease associated with CS pathogens and those without bacteraemia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06229-x.

Differential effects of chromosome and plasmid blaCTX-M-15 genes on antibiotic susceptibilities in extended-spectrum beta-lactamase-producing Escherichia coli isolates from patients with urinary tract infection

OBJECTIVES

To compare antibiotic susceptibilities between chromosomal and plasmid bla_CTX-M-15 locations in urinary tract infection-causing extended-spectrum β-lactamases-producing Escherichia coli bla_CTX-M-15 isolated in Indonesia.

METHODS

A total of 84 strains identified as extended-spectrum β-lactamases-producing E. coli were isolated from patients with urinary tract infection in Indonesia in 2015. Antimicrobial susceptibility tests were performed on these strains using 18 antibiotics, and extended-spectrum β-lactamase bla genes were detected by polymerase chain reaction. Gene localization of bla_CTX-M-15 -positive strains was confirmed by Southern blot hybridization, and epidemiological typing was conducted using multilocus sequence typing.

RESULTS

Of 54 strains harboring the bla_CTX-M-15 gene, 27 showed localization on chromosome, 20 on plasmid, and seven on chromosome and plasmid. Most multilocus sequence typing sequence types of the 27 strains with chromosomal bla_CTX-M-15 were ST405 (25.9%) and ST131 (22.2%) strains, whereas the 20 strains with plasmid-bla_CTX-M-15 were mostly ST410 (55.0%).

CONCLUSIONS

Extended-spectrum β-lactamases-producing E. coli bla_CTX-M-15 with plasmid genes show significantly higher resistant rates against piperacillin-tazobactam but lower resistant rates against chloramphenicol compared to chromosomal strains in Indonesian patients with urinary tract infection. Mechanistic investigations will be necessary to advance our knowledge of antimicrobial resistance in urinary tract infection.

High plasmid variability, and the presence of IncFIB, IncQ, IncA/C, IncHI1B, and IncL/M in clinical isolates of Klebsiella pneumoniae with bla KPC and bla NDM from patients at a public hospital in Brazil

INTRODUCTION

Antibiotic resistance in carbapenemase-producing Klebsiella pneumoniae is acquired and disseminated mainly by plasmids. Therefore, we aimed to investigate the occurrence of carbapenemase genes, analyze the genetic diversity by ERIC-PCR, and examine the most common plasmid incompatibility groups (Incs) in clinical isolates of K. pneumoniae from colonization and infection in patients from a hospital in Brazil.

METHODS

Twenty-seven isolates of carbapenem-resistant K. pneumoniae were selected and screened for the presence of carbapenemase genes and Incs by PCR, followed by amplicon sequencing.

RESULTS

The bla_KPC and bla_NDM genes were detected in 24 (88.8 %) and 16 (59.2 %) of the isolates, respectively. Thirteen isolates (48.1 %) were positive for both genes. The IncFIB (92.6 %) and IncQ (88.8 %) were the most frequent plasmids, followed by IncA/C, IncHI1B, and IncL/M, indicating that plasmid variability existed in these isolates. To our knowledge, this is the first report of IncHI1B in Brazil. We found eight isolates with clonal relationship distributed in different sectors of the hospital.

CONCLUSIONS

The accumulation of resistance determinants, the variability of plasmid Incs, and the clonal dissemination detected in K. pneumoniae isolates demonstrate their potential for infection, colonization, and the dissemination of different resistance genes and plasmids.

Clinical impact of endemic NDM-producing Klebsiella pneumoniae in intensive care units of the national referral hospital in Jakarta, Indonesia

OBJECTIVE

A prospective observational study was performed to assess the epidemiology and clinical impact of carbapenem-non-susceptible Klebsiella pneumoniae (CNKP) in intensive care units (ICUs) of the national referral hospital in Jakarta, Indonesia.

MATERIALS/METHODS

Adult patients consecutively hospitalized for > 48 h in two ICUs of the national referral hospital were included from April until October 2013 and from April until August 2014. K. pneumoniae from clinical cultures and standardized screening of rectum and throat on admission, discharge and weekly if hospitalized > 7 days were collected. Environmental niches and healthcare workers (HCWs) were also screened. Susceptibility was determined phenotypically and the presence of carbapenemase genes by PCR. Raman spectroscopy as well as multiple-locus variable number tandem repeat analysis (MLVA) were used for typing.

RESULTS

Twenty-two out of 412 (5.3%) patients carried CNKP on admission and 37/390 (9.5%) acquired CNKP during ICU stay. The acquisition rate was 24.7/1000 patient-days at risk. One out of 31 (3.2%) environmental isolates was a CNKP. None of the HCWs carried CNKP. Acquisition of CNKP was associated with longer ICU stay (adjusted Hazard Ratio: 2.32 [CI₉₉: 1.35-3.68]). ICU survival was lower among patients with CNKP compared to patients with carbapenem-susceptible K. pneumoniae (aHR 2.57, p = 0.005). Ninety-six of the 100 (96%) CNKP isolates carried a carbapenemase gene, predominantly bla_NDM. Raman typing revealed three major clusters among 48 Raman types identified, whereas MLVA distinguished six major clusters among a total of 30 different genotypes.

CONCLUSIONS

NDM-producing CNKP are introduced into these ICUs and some strains expand clonally among patients and the environment, resulting in endemic CNKP. CNKP acquisition was associated with prolonged ICU stay and may affect ICU survival.

TRIAL REGISTRATION

The study was registered at Netherlands Trial Register http://www.trialregister.nl. Candidate number: 23527, NTR number: NTR5541, NL number: NL5425 (https://www.trialregister.nl/trial/5424), Retrospectively registered: NTR: 22 December 2015.

Intra-hospital acquisition of colonization and infection by Klebsiella pneumoniae strains producing carbapenemases and carriage evolution: A longitudinal analysis in an Italian teaching hospital from January 2017 to August 2019

OBJECTIVES

We present an updated picture (1/1/2017-31/08/2019) of the frequency of carbapenemase producing Klebsiella pneumoniae (CPKP) in surveillance rectal swabs (SRS) and in clinical samples (CS) of patients admitted to a tertiary level hospital, focusing on longitudinal evolution of CPKP detected in SRS and on colistin resistant strains.

METHODS

Retrospective longitudinal analysis. Only the first positive CPKP strain isolated from each patient was included.

RESULTS

638 CPKP strains were identified (471 in SRS and 167 in CS). SRS frequency increased over time in the medical department, remained high in the surgical department (SD) and decreased in the intensive care department. Most SRS-71.3%-and 49.1% of CS had nosocomial origin; about half of the SRS were identified in the SD. Regarding SRS evolution, carriage was confirmed in 39.5% of patients, no more testing in 25.5%, clinical involvement in 24.8 %, and negative result in 10.2%. Rates of colistin resistance were 20.1% in 2017, 31.2% in 2018 and 26.9% in 2019.

CONCLUSIONS

CPKP diffusion is still an important issue despite the surveillance program. It is vital to enhance medical staff's awareness on this because most CPKP first detections in SRS occurred during hospital stay due to a nosocomial acquisition with a comparable picture over time. Colistin resistance is increasing.