Bloodstream Infections at Two Neonatal Intensive Care Units in Ghana: Multidrug Resistant Enterobacterales Undermine the Usefulness of Standard Antibiotic Regimes

Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana

OBJECTIVES

Comprehensive data on the genomic epidemiology of hospital-associated Klebsiella pneumoniae in Ghana are scarce. This study investigated the genomic diversity, antimicrobial resistance patterns, and clonal relationships of 103 clinical K. pneumoniae isolates from five tertiary hospitals in Southern Ghana-predominantly from paediatric patients aged under 5 years (67/103; 65%), with the majority collected from urine (32/103; 31%) and blood (25/103; 24%) cultures.

METHODS

We generated hybrid Nanopore-Illumina assemblies and employed Pathogenwatch for genotyping via Kaptive [capsular (K) locus and lipopolysaccharide (O) antigens] and Kleborate (antimicrobial resistance and hypervirulence) and determined clonal relationships using core-genome MLST (cgMLST).

RESULTS

Of 44 distinct STs detected, ST133 was the most common, comprising 23% of isolates (n = 23/103). KL116 (28/103; 27%) and O1 (66/103; 64%) were the most prevalent K-locus and O-antigen types. Single-linkage clustering highlighted the global spread of MDR clones such as ST15, ST307, ST17, ST11, ST101 and ST48, with minimal allele differences (1-5) from publicly available genomes worldwide. Conversely, 17 isolates constituted novel clonal groups and lacked close relatives among publicly available genomes, displaying unique genetic diversity within our study population. A significant proportion of isolates (88/103; 85%) carried resistance genes for ≥3 antibiotic classes, with the blaCTX-M-15 gene present in 78% (n = 80/103). Carbapenem resistance, predominantly due to blaOXA-181 and blaNDM-1 genes, was found in 10% (n = 10/103) of the isolates.

CONCLUSIONS

Our findings reveal a complex genomic landscape of K. pneumoniae in Southern Ghana, underscoring the critical need for ongoing genomic surveillance to manage the substantial burden of antimicrobial resistance.

Clinical characteristics and risk factors for neonatal bloodstream infection due to carbapenem-resistant Enterobacteriaceae: A single-centre Chinese retrospective study

OBJECTIVES

To analyse the clinical characteristics and risk factors for bloodstream infections (BSIs) caused by carbapenem-resistant Enterobacteriaceae (CRE) in neonates.

METHODS

This single-centre, retrospective study included all patients with BSIs admitted to a neonatal intensive care unit between 1 January 2015 and 30 April 2022. The clinical and microbiological data of patients were collected; predictors of 30-day mortality in patients with CRE BSIs were also identified in this study.

RESULTS

Among the 224 neonates with Enterobacteriaceae BSIs, 39.29% (88/224) of the patients developed CRE BSIs. The 30-day mortality rate reached up to 21.59% (19/88). The Quick Sequential Organ Failure Assessment score > 2 (odds ratio [OR] and 95% credibility interval [CI]: 3.852 [1.111-13.356], P < 0.05), prior to more than two kinds of antibiotics use (OR and 95% CI: 9.433 [1.562-56.973], P < 0.05), pneumonia (OR and 95% CI: 3.847 [1.133-13.061], P < 0.05), and caesarean section (OR and 95% CI: 2.678 [1.225-5.857], P < 0.05) were independent risk factors associated with CRE BSIs. Moreover, the risk factors for mortality in neonates with CRE BSIs were significantly associated with neonatal Sequential Organ Failure Assessment score > 6 (OR and 95% CI: 16.335 [1.446-184.517], P < 0.05).

CONCLUSION

Prior to more than two kinds of antibiotics use, Quick Sequential Organ Failure Assessment score > 2, pneumonia and caesarean section were independent risk factors for CRE BSIs. The Neonatal Sequential Organ Failure Assessment score > 6 was a risk factor for mortality associated with CRE BSIs.

Antimicrobial resistance in Enterobacterales infections among children in sub-Saharan Africa: a systematic review and meta-analysis

Background

The burden of antimicrobial resistance (AMR) has been estimated to be the highest in sub-Saharan Africa (SSA). The current study estimated the proportion of drug-resistant Enterobacterales causing infections in SSA children.

Methods

We searched MEDLINE/PubMed, Embase and the Cochrane Library to identify retrospective and prospective studies published from 01/01/2005 to 01/06/2022 reporting AMR of Enterobacterales causing infections in sub-Saharan children (0-18 years old). Studies were excluded if they had unclear documentation of antimicrobial susceptibility testing methods or fewer than ten observations per bacteria. Data extraction and quality appraisal were conducted by two authors independently. The primary outcome was the proportion of Enterobacterales resistant to antibiotics commonly used in paediatrics. Proportions were combined across studies using mixed-effects logistic regression models per bacteria and per antibiotic. Between-study heterogeneity was assessed using the I2 statistic. The protocol was registered with PROSPERO (CRD42021260157).

Findings

After screening 1111 records, 122 relevant studies were included, providing data on more than 30,000 blood, urine and stool isolates. Escherichia coli and Klebsiella spp. were the predominant species, both presenting high proportions of resistance to third-generation cephalosporins, especially in blood cultures: 40.6% (95% CI: 27.7%-55%; I2: 85.7%, number of isolates (n): 1032) and 84.9% (72.8%-92.2%; I2: 94.1%, n: 2067), respectively. High proportions of resistance to other commonly used antibiotics were also observed. E. coli had high proportions of resistance, especially for ampicillin (92.5%; 95% CI: 76.4%-97.9%; I2: 89.8%, n: 888) and gentamicin (42.7%; 95% CI: 30%-56.5%; I2: 71.9%, n: 968). Gentamicin-resistant Klebsiella spp. were also frequently reported (77.6%; 95% CI: 65.5%-86.3%; I2: 91.6%, n: 1886).

Interpretation

High proportions of resistance to antibiotics commonly used for empirical treatment of infectious syndromes were found for Enterobacterales in sub-Saharan children. There is a critical need to better identify local patterns of AMR to inform and update clinical guidelines for better treatment outcomes.

Funding

No funding was received.

Klebsiella pneumoniae ST147 harboring blaNDM-1, multidrug resistance and hypervirulence plasmids

The spread of hypervirulent (hv) and carbapenem-/multidrug-resistant Klebsiella pneumoniae is an emerging problem in healthcare settings. The New Delhi metallo-β-lactamase-1 (blaNDM-1) is found in Enterobacteriaceae including K. pneumoniae. The blaNDM-1 is capable of hydrolyzing β-lactam antibiotics which are used for treatment of severe infections caused by multidrug-resistant Gram-negative bacteria. This is associated with the unacceptably high mortality rate in immunocompromised burn injury patients. This study reports on the characterization of blaNDM-1 gene and virulence factors in hv carbapenem-/multidrug-resistant K. pneumoniae ST147 in the burns unit of a tertiary teaching hospital during routine surveillance. Two K. pneumoniae strains were obtained from wounds of burn-infected patients from May 2020 to July 2021. The hypervirulence genes and genetic context of the blaNDM-1 gene and mobile genetic elements potentially involved in the transposition of the gene were analyzed. We identified a conserved genetic background and an IS26 and open reading frame flanking the blaNDM-1 gene that could suggest its involvement in the mobilization of the gene. The plasmid harbored additional antibiotic resistance predicted regions that were responsible for resistance to almost all the routinely used antibiotics. To ensure the identification of potential outbreak strains during routine surveillance, investigations on resistance genes and their environment in relation to evolution are necessary for molecular epidemiology.IMPORTANCEData obtained from this study will aid in the prompt identification of disease outbreaks including evolving resistance and virulence of the outbreak bacteria. This will help establish and implement antimicrobial stewardship programs and infection prevention protocols in fragile health systems in countries with limited resources. Integration of molecular surveillance and translation of whole-genome sequencing in routine diagnosis will provide valuable data for control of infection. This study reports for the first time a high-risk clone K. pneumoniae ST147 with hypervirulence and multidrug-resistance features in Ghana.

Etiology of Bacterial Sepsis and Isolate Resistance Patterns in Hospitalized Neonates in Zambia

BACKGROUND

The Sepsis Prevention in Neonates in Zambia study is a prospective cohort study that evaluated an infection prevention and control (IPC) bundle in the University Teaching Hospital neonatal intensive care unit (NICU) in Lusaka, Zambia. We present here the etiologies, antimicrobial resistance profiles, and associated mortality of bloodstream infections (BSI) in this cohort.

METHODS

Venous blood was collected from neonates with clinically suspected sepsis and cultured with an automated blood culture system. Organism identification and susceptibility testing were done using the Vitek II system. We used the CDC National Health Safety Network criteria to define pathogens and commensals.

RESULTS

There were 1120 blood cultures performed for 1060 neonates with suspected sepsis. Overall, 38% (424/1120) of cultures were positive of which 72% (306/424) grew pathogens. Blood cultures obtained after, as compared to before, 2 days of hospitalization were more likely to yield a pathogen (77% vs. 65%; P < 0.001). Klebsiella pneumoniae was the most prevalent organism, accounting for 74% (225/306) of all pathogens . K. pneumoniae isolates were highly resistant: 98% (221/225) were extended-spectrum beta-lactamase (ESBL)-positive, while 81% were resistant to gentamicin (182/225) and fluoroquinolones (177/219). Only one isolate was carbapenem resistant. Observed mortality rate was 32% (122/380); 61% (75/122) of the deaths was related to Klebsiella BSI.

CONCLUSIONS

Multidrug-resistant ESBL-producing Klebsiella species were the main organisms responsible for BSI and were associated with increased mortality. BSI risk increased with prolonged hospitalization, underscoring the importance of IPC measures in the NICU.

Infection prevention and control in neonatal units: An ethnographic study of social and clinical interactions among healthcare providers and mothers in Ghana

INTRODUCTION

Healthcare-associated infections (HAIs) are a global health challenge, particularly in low- and middle-income countries (LMICs). Infection prevention and control (IPC) remains an important strategy for preventing HAIs and improving the quality of care in hospital wards. The social environment and interactions in hospital wards are important in the quest to improve IPC. This study explored care practices and the interactions between healthcare providers and mothers in the neonatal intensive care units (NICU) in two Ghanaian hospitals and discusses the relevance for IPC.

METHODOLOGY

This study draws on data from an ethnographic study using in-depth interviews, focus group discussions involving 43 healthcare providers and 72 mothers, and participant observations in the wards between September 2017 and June 2019. The qualitative data were analysed thematically using NVivo 12 to facilitate coding.

FINDINGS

Mothers of hospitalized babies faced various challenges in coping with the hospital environment. Mothers received sparse information about their babies' medical conditions and felt intimidated in the contact with providers. Mothers strategically positioned themselves as learners, guardians, and peers to enable them to navigate the clinical and social environment of the wards. Mothers feared that persistent requests for information might result in their being labelled "difficult mothers" or might impact the care provided to their babies. Healthcare providers also shifted between various positionings as professionals, caregivers, and gatekeepers, with the tendency to exercise power and maintain control over activities on the ward.

CONCLUSION

The socio-cultural environment of the wards, with the patterns of interaction and power, reduces priority to IPC as a form of care. Effective promotion and maintenance of hygiene practices require cooperation, and that healthcare providers and mothers find common grounds from which to leverage mutual support and respect, and through this enhance care for mothers and babies, and develop stronger motivation for promoting IPC.

New Antimicrobials for the Treatment of Neonatal Sepsis Caused by Multi-Drug-Resistant Bacteria: A Systematic Review

BACKGROUND

Infections by multi-drug-resistant (MDR) organisms are sharply increasing in newborns worldwide. In low and middle-income countries, a disproportionate amount of neonatal sepsis caused by MDR Gram negatives was recently reported. Newborns with infections by MDR organisms with limited treatment options may benefit from novel antimicrobials.

METHODS

We performed a literature search investigating the use in newborns, infants and children of novel antimicrobials for the treatment of MDR Gram negatives, namely ceftazidime/avibactam, ceftolozane/tazobactam, cefiderocol, meropenem/vaborbactam, imipenem/relebactam, and Gram positives with resistance of concern, namely ceftaroline and dalbavancin. PubMed, EMBASE, and Web of Science were searched.

RESULTS

A total of 50 records fulfilled the inclusion criteria. Most articles were case reports or case series, and ceftazidime/avibactam was the most studied agent. All studies showed favorable efficacy and safety profile in newborns and across different age cohorts.

CONCLUSIONS

novel antibiotics may be considered in newborns for the treatment of MDR Gram negatives with limited treatment options and for Gram positives with resistance concerns. Further studies are needed to address their effectiveness and safety in newborns.

Multicenter Surveillance of Antimicrobial Resistance among Gram-Negative Bacteria Isolated from Bloodstream Infections in Ghana

BACKGROUND

Antimicrobial resistance (AMR) in Gram-negative bacteria-causing bloodstream infections (BSIs), such as Klebsiella pneumoniae and non-typhoidal Salmonella (NTS), is a major public health concern. Nonetheless, AMR surveillance remains scarce in sub-Saharan Africa, where BSI treatment is largely empirical. The aim of the study was to determine the distribution and AMR patterns of BSI-causing NTS, K. pneumoniae, and other Gram-negative bacteria in Ghana.

METHODS

A cross-sectional study was conducted between April and December 2021 at eleven sentinel health facilities across Ghana as part of a pilot study on the feasibility and implementation of the human sector AMR surveillance harmonized protocol in sub-Saharan Africa. Gram-negative bacteria recovered from blood specimens of febrile patients were identified using MALDI-TOF and evaluated for antimicrobial resistance using the BD Phoenix M50 analyzer and Kirby-Bauer disc diffusion. The Department of Medical Microbiology at the University of Ghana served as the reference laboratory.

RESULTS

Out of 334 Gram-negative blood isolates, there were 18 (5.4%) NTS, 85 (25.5%) K. pneumoniae, 88 (26.4%) Escherichia coli, 40 (12.0%) Acinetobacter baumannii, 25 (7.5%) Pseudomonas aeruginosa, and 77 (23.1%) other Gram-negative bacteria. As a composite, the isolates displayed high resistance to the antibiotics tested-amoxicillin (89.3%), tetracycline (76.1%), trimethoprim-sulfamethoxazole (71.5%), and chloramphenicol (59.7%). Resistance to third-generation cephalosporins [ceftriaxone (73.7%), cefotaxime (77.8%), and ceftazidime (56.3%)] and fluoroquinolones [ciprofloxacin (55.3%)] was also high; 88% of the isolates were multidrug resistant, and the rate of extended-spectrum beta-lactamase (ESBL) production was 44.6%. Antibiotic resistance in K. pneumoniae followed the pattern of all Gram-negative isolates. Antibiotic resistance was lower in NTS blood isolates, ranging between 16.7-38.9% resistance to the tested antibiotics. Resistance rates of 38.9%, 22.2%, and 27.8% were found for cefotaxime, ceftriaxone, and ceftazidime, respectively, and 27.8% and 23.8% for ciprofloxacin and azithromycin, respectively, which are used in the treatment of invasive NTS. The prevalence of multidrug resistance in NTS isolates was 38.9%.

CONCLUSIONS

Multicenter AMR surveillance of Gram-negative blood isolates from febrile patients was well-received in Ghana, and the implementation of a harmonized protocol was feasible. High resistance and multidrug resistance to first- or second-choice antibiotics, including penicillins, third-generation cephalosporins, and fluoroquinolones, were found, implying that these antibiotics might have limited effectiveness in BSI treatment in the country. Continuation of AMR surveillance in Gram-negative blood isolates is essential for a better understanding of the extent of AMR in these pathogens and to guide clinical practice and policymaking.

Healthcare-Associated Infection Prevention Interventions for Neonates in Resource-Limited Settings

Healthcare-associated infections (HAIs) and antimicrobial-resistant (AMR) infections are leading causes of neonatal morbidity and mortality, contributing to an extended hospital stay and increased healthcare costs. Although the burden and impact of HAI/AMR in resource-limited neonatal units are substantial, there are few HAI/AMR prevention studies in these settings. We reviewed the mechanism of action and evidence supporting HAI/AMR prevention interventions, including care bundles, for hospitalized neonates in low- and middle-income countries (LMIC).