Colonisation with extended spectrum beta-lactamase-producing and carbapenem-resistant Enterobacterales in children admitted to a paediatric referral hospital in South Africa

Emergence and expansion of carbapenem resistant enterobacterales in the Western Cape Province, South Africa

BACKGROUND

Carbapenem resistant Enterobacterales (CRE) have become established as leading pathogens in South African healthcare facilities. The aim of this study is to describe the epidemiology of CRE carriage and clinical infection episodes at healthcare facilities in the Western Cape Province of South Africa (2016-2020), and identify factors associated with mortality in CRE infected patients.

METHODOLOGY

We used routine data from the Provincial Health Data Centre to track the emergence of CRE in healthcare facilities in the Western Cape Province of South Africa. We included all CRE episodes (clinical and carriage) at Western Cape hospitals (including day and inpatients) from 2016 to 2020 to determine the distribution of CRE, patient demographics and antibiotic resistance phenotypes. Logistic regression was performed to identify factors associated with mortality from clinical CRE episodes.

RESULTS

2242 CRE episodes (1580 [70.5%] clinical and 662 [29.5%] carriage) were identified. From these, 2281 CRE isolates were identified, with Klebsiella species predominating (1644, 72.1%). Affected patients had a median age of 31 (IQR 0-52) years, and 1167 (52.0%) were male. Most CRE episodes were recorded in central hospitals (70.0%, p < 0.001). Where outcome data was available, crude in-hospital mortality rates were 26.9% (371/1379) for CRE clinical episodes versus 6.4% (41/640) for CRE carriage episodes (p < 0.001). Factors that showed a statistically significant association with in-hospital mortality were female sex [adjusted odd ratio (aOR) 1.40 (95% confidence interval (CI) 1.09-1.560)], adult patients [aOR 1.76 (95% CI 1.20-2.57)], CRE isolation from a sterile specimen [aOR 0.41 (95% CI 0.32-0.53)], and >3 days between hospital admission and specimen collection [aOR 1.56 (95% CI 1.11-2.18)].

CONCLUSIONS

CRE episodes at Western Cape healthcare facilities are concentrated at tertiary hospitals, with high case fatality rates in patients with clinical CRE episodes. Infection control interventions must be strengthened to reduce transmission of CRE, and to reduce infection risks.

Prevalence of rectal carbapenem resistant Enterobacterales carriage among patients attending healthcare facilities in Ibadan, Nigeria: a descriptive study

BACKGROUND

Carbapenem Resistant Enterobacterales (CRE) infections are increasingly associated with or directly responsible for morbidity and mortality from bacterial infections in sub-Saharan Africa where there are limited antibiotic options. CRE rectal colonization of patients in healthcare facilities provides a reservoir of these organisms and could potentially cause invasive infections in these settings. The prevalence of rectal carriage among patients attending healthcare facilities in Nigeria has not been previously described. We set out to assess the prevalence of rectal CRE carriage and their antibiotic susceptibility patterns among patients attending healthcare facilities in Nigeria.

METHODS

A descriptive cross-sectional study was carried out from December 2021 to September 2022 in Ibadan, in which patients attending primary, secondary and tertiary healthcare facilities were screened for rectal carriage of CRE by microscopy, culture and sensitivity of rectal swab specimens.

RESULTS

A total of 291 patients were screened; 45 (15.5%), 66 (22.7%) and 180 (61.8%) at primary, secondary and tertiary healthcare facilities, respectively. All but one of them had received a third-generation cephalosporin or carbapenem in the preceding 30 days. The mean age was 28.8 years and 55.7% were male. Overall, 51 (17.5%) participants had CRE colonization, with 5(11.1%), 9(13.6%) and 37(20.6%) at primary, secondary and tertiary healthcare facilities, respectively (p = 0.243). Regarding antimicrobial susceptibility, 43(84.3%) CRE isolates were resistant to at least 3 different classes of antibiotics while two Escherichia coli isolates were resistant to all 5 classes of antibiotics tested. The lowest rates of CRE resistance were to tigecycline (6, 11.5%) and colistin (8, 15.7%).

CONCLUSIONS

In this first study on CRE colonization in Nigeria, we found that a substantial proportion of patients in three levels of healthcare facilities had rectal carriage of CRE, including pan-resistant isolates. Active surveillance and appropriate infection prevention and control practices (IPC) need to be urgently strengthened to mitigate the risk of active CRE infection.

TRIAL REGISTRATION

Not applicable.

Genomic characterization of multi drug resistant ESBL-producing Escherichia coli isolates from patients and patient environments in a teaching hospital in Ghana

BACKGROUND

ESBL-producing Escherichia coli pose a growing health risk in community and healthcare settings. We investigated the resistome, virulome, mobilome, and genetic relatedness of multidrug-resistant (MDR) E. coli isolates from patients and their environment in a Ghanaian teaching hospital.

MATERIALS AND METHODS

Twenty-three MDR ESBL-producing or carbapenem-resistant E. coli isolates from a collection of MDR Gram-negative bacteria (GNB) from patients and environments were selected for genomic analyses. Whole genome sequencing and bioinformatics tools were used to analyze genomic characteristics and phylogeny.

RESULTS

The prevalence and incidence of rectal carriage of ESBL E. coli among patients were 13.65% and 11.32% respectively. The β-lactamase genes, blaTEM-1B (10 isolates) and blaCTX-M-15 (12 isolates) were commonly associated with IncFIB plasmid replicons and co-occurred with aminoglycoside, macrolide, and sulfamethoxazole/trimethoprim resistance. Insertion sequences, transposons, and class I integrons were found with blaCTX-M-15. Carriage and environmental isolates carried multiple virulence genes, with terC being the most prevalent in 21 isolates. Seventeen sequence types (STs) were identified, including a novel ST (ST13846). Phylogenetic analysis grouped the isolates into four main clusters, with one outlier. High genetic relatedness was observed between two carriage isolates of ST940 and between a carriage isolate and an environmental isolate of ST648. Isolates with different STs, collected at different times and locations, also showed genetic similarities.

CONCLUSION

We identified ESBL-producing E. coli with diverse genomic characteristics circulating in different hospital directorates. Clonal relatedness was observed among isolates from patients and the environment, as well as between different patients, suggesting transmission within and between sources.

The Importance of Carbapenemase-Producing Enterobacterales in African Countries: Evolution and Current Burden

Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug-resistant organisms (MDROs) can spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial for MDRO dissemination, colonizing microbes can lead to symptomatic infections in carriers. Carbapenemase-producing Enterobacterales (CPE) are among the most important MDROs involved in colonizations and infections with severe outcomes. This review aimed to track down the first reports of CPE in Africa, describe their dissemination throughout African countries and summarize the current status of CRE and CPE data, highlighting current knowledge and limitations of reported data. Two database queries were undertaken using Medical Subject Headings (MeSH), employing relevant keywords to identify articles that had as their topics beta-lactamases, carbapenemases and carbapenem resistance pertaining to Africa or African regions and countries. The first information on CPE could be traced back to the mid-2000s, but data for many African countries were established after 2015-2018. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE infections and colonizations are present in most African countries and that carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.

Fecal Carriage of Carbapenem Resistant Enterobacterales and Associated Factors Among Admitted Patients in Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia

Purpose

The Enterobacterales family colonizes the human gut as normal flora in all age groups, with bacterial infections being the most common cause. Resistance is currently observed in all normal flora. The aim of this study was to determine the frequency of fecal carriage of carbapenem-resistant Enterobacterales (CRE), carbapenemase-producing Enterobacterales (CPE), and associated factors in the faeces of admitted patients.

Methods

A cross-sectional study was conducted in Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia. A total of 384 rectal swabs were collected from various wards in admitted patients who have consented to participate. The specimens were inoculated on a MacConkey agar plate, and then they were incubated at 37 °C for 18 to 24 hours. Using the BD PhoenixTM M50 compact system identification and antimicrobial susceptibility testing were performed. Using the modified carbapenem inactivation method, it was determined whether the carbapenem-resistant bacterial isolate produced carbapenemase or not.

Results

Overall prevalence of carbapenem-resistant Enterobacterales carriage and carbapenemase producing Enterobacterales in admitted patients was 17.2% (95%, Confidence Interval: 13.3-21.1%) and 7% (95%, Confidence Interval: 4.7-9.9%), respectively. The predominate carbapenem-resistant Enterobacterales in fecal carriage was K. pneumoniae, 15.4% (23/149), E. cloacae 15.4% (6/39), followed by E. coli 12.4% (37/307) of carbapenem-resistant Enterobacterales (CRE) isolate. Carbapenem-resistant Enterobacterales carriage isolates showed large level of resistance to ciprofloxacin, and sulfamethoxazole-trimethoprim. Prior intake of antibiotics (Odds Ratio 2.42, 95% CI: 11.186-4.95) was significantly associated with higher carbapenem-resistant Enterobacterales carriage.

Conclusion

We observed a high prevalence of carbapenem-resistant Enterobacterales carriage and carbapenemase-producing Enterobacterales among admitted patients. There were only amikacin and colistin that could be effective for carbapenem-resistant Enterobacterales isolates. Hence, the control of carbapenem-resistant Enterobacterales carriage should be given priority by carbapenem-resistant Enterobacterales screening for fecal of admitted patients, and adhering to good infection prevention practice in hospital settings.

Antimicrobial Susceptibility Among Gram-Negative Isolates in Pediatric Patients in Latin America, Africa-Middle East, and Asia From 2016-2020 Compared to 2011-2015: Results From the ATLAS Surveillance Study

BACKGROUND

Antimicrobial resistance (AMR) data in the pediatric population are limited, particularly in developing countries. This study assessed the AMR profile and key resistance phenotypes and genotypes for Gram-negative bacteria (GNB) isolates collected as part of the Antimicrobial Testing Leadership and Surveillance program from pediatric patients in Latin America, Africa-Middle East, and Asia in 2016-2020 versus 2011-2015.

METHODS

Minimum inhibitory concentrations by broth microdilution methodology were interpreted per the Clinical and Laboratory Standards Institute. European Committee on Antimicrobial Susceptibility Testing breakpoints were used for interpreting colistin activity. β-lactamase genes were screened by polymerase chain reaction and sequencing.

RESULTS

For Acinetobacter baumannii, low susceptibility (<60.0%) was observed for all antimicrobials, except colistin (≥92.9%), across regions and year periods. Ceftazidime-avibactam, amikacin, colistin, and meropenem were mostly active (78.6%-100.0%) against Enterobacter cloacae, Escherichia coli, and Klebsiella pneumoniae. For Pseudomonas aeruginosa, susceptibility to ceftazidime-avibactam, amikacin, and colistin was ≥85.9%. Among resistance phenotypes, carbapenem-resistant (CR, ≥44.8%) and difficult-to-treat resistant (DTR, ≥37.1%) rates were the highest in A. baumannii. A consistent increase in CR and DTR K. pneumoniae was noted across regions over time. Extended-spectrum β-lactamases (ESBL)-producing K. pneumoniae (32.6%-55.6%) were more frequent than ESBL-producing E. coli (25.3%-37.1%). CTX-M was the dominant ESBL among Enterobacterales. NDM-positive Enterobacterales species and VIM-positive P. aeruginosa were identified across regions.

CONCLUSIONS

This study identified high susceptibility to few agents for key GNB in pediatric patients. Continued surveillance of resistance phenotypes and genotypes at regional levels may help to guide appropriate treatment decisions.

Gastrointestinal colonization of Extended-Spectrum Beta lactamase producing bacteria among children below five years of age hospitalized with fever in Dar es Salaam, Tanzania

BACKGROUND

Gastrointestinal colonization of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) is of concern because prior colonization increases risk for subsequent infections. To date, the link between ESBL-PE fecal carriage and the risk of subsequent ESBL-PE infection has not been well established, and information on carriage of such pathogens among children with invasive infections such as blood stream infections (BSI) remains to be explored worldwide.

METHODS

This cross-sectional study was conducted among childrenunder the age of 5 years admitted for febrile illness in Dar es Salaam, Tanzania, between March 2017 and July 2018. We used rectal swabs to screen for ESBL-PE using selective media, ChromID® ESBL. Bacterial isolates were identified by MALDI-TOF.Blood cultures were drawn from all children. Antimicrobial susceptibility testingwas done using disk diffusion method. ESBL alleles were identified by Real-Time PCR and sequencing.

RESULTS

The overall prevalence of ESBL-PE carriage was 56% (112/200) and washighestamong children 4-6 months old (17/21, 81%) (p =0.05). Children with BSI had high ESBL-PE carriage (78.4%) compared to those without BSI (53.1%)(p=0.02; AOR 3.4, 95% CI1.20-9.58).The most common isolate was E.coli (64/112, 45%). Sixteen pairs of ESBL-PEisolates(from the gut and from blood)had similar antimicrobial susceptibility profile. We detectedbla_CTX-M gene in 97% of all phenotypically detected ESBL-PE; among those,bla_CTX-M-15 was dominant (99%).

CONCLUSIONS

We report a high prevalence of ESBL-PEfecal carriage among children with BSI in Tanzania. Colonization of ESBL-PEwasa risk factor for ESBL-BSI.

High Fecal Carriage of Multidrug Resistant Bacteria in the Community among Children in Northwestern Tanzania

Colonization of multidrug resistant (MDR) bacteria is associated with subsequent invasive infections in children with comorbidities. This study aimed to determine the resistance profile and factors associated with MDR pathogen colonization among HIV−and HIV+ children below five years of age in Mwanza, Tanzania. A total of 399 (HIV− 255 and HIV+ 144) children were enrolled and investigated for the presence of MDR bacteria. The median [IQR] age of children was 19 (10–36) months. Out of 27 Staphylococcus aureus colonizing the nasal cavity, 16 (59.5%) were methicillin resistant while 132/278 (47.2%) of Enterobacteriaceae from rectal swabs were resistant to third generation cephalosporins, with 69.7% (92/132) exhibiting extended spectrum beta lactamase (ESBL) phenotypes. The proportion of resistance to gentamicin, amoxicillin/clavulanic acid and meropenem were significantly higher among HIV+ than HIV− children. A history of antibiotic use in the last month OR 2.62 [1.1, 6.9] (p = 0.04) and history of a relative admitted from the same household in the past three months OR 3.73 [1.1, 13.2] (p = 0.03) independently predicted ESBL rectal colonization. HIV+ children had significantly more fecal carriage of isolates resistant to uncommonly used antibiotics. There is a need to strengthen antimicrobial stewardship and Infection Prevention and Control (IPC) programs to prevent the emergence and spread of MDR pathogens in children.

Molecular Epidemiology of Extended-Spectrum Beta-Lactamase and AmpC Producing Enterobacteriaceae among Sepsis Patients in Ethiopia: A Prospective Multicenter Study

Extended-spectrum beta-lactamases (ESBLs) and AmpC producing Enterobacteriaceae are public health threats. This study aims to characterize ESBL and AmpC producing Enterobacteriaceae isolated from sepsis patients. A multicenter study was conducted at four hospitals located in central (Tikur Anbessa and Yekatit 12), southern (Hawassa) and northern (Dessie) parts of Ethiopia. Blood culture was performed among 1416 sepsis patients. Enterobacteriaceae (n = 301) were confirmed using MALDI-TOF and subjected for whole genome sequencing using the Illumina (HiSeq 2500) system. The overall genotypic frequencies of ESBL and AmpC producing Enterobacteriaceae were 75.5% and 14%, respectively. The detection of ESBL producing Enterobacteriaceae at Hawassa, Yekatit 12, Tikur Anbessa and Dessie was 95%, 90%, 82% and 55.8%, respectively. The detection frequency of bla_CTX-M, bla_TEM and bla_SHV genes was 73%, 63% and 33%, respectively. The most frequently detected ESBL gene was bla_CTX-M-15 (70.4%). The common AmpC genes were bla_ACT (n = 22) and bla_CMY (n = 13). Of Enterobacteriaceae that harbored AmpC (n = 42), 71% were ESBL co-producers. Both bla_TEM-1B (61.5%) and bla_SHV-187 (27.6%) were the most frequently detected variants of bla_TEM and bla_SHV, respectively. The molecular epidemiology of ESBL producing Enterobacteriaceae showed high frequencies and several variants of ESBL and AmpC genes. Good antimicrobial stewardship and standard bacteriological laboratory services are necessary for the effective treatment of ESBL producing Enterobacteriaceae.