Antimicrobial resistance detection in Southeast Asian hospitals is critically important from both patient and societal perspectives, but what is its cost?

The barriers and facilitators of implementing a national laboratory-based AMR surveillance system in Cambodia: key informants' perspectives and assessments of microbiology laboratories

Background

Collecting data on antimicrobial resistance (AMR) is an essential approach for defining the scope of the AMR problem, developing evidence-based interventions and detecting new and emerging resistances. Our study aimed to identify key factors influencing the implementation of a laboratory-based AMR surveillance system in Cambodia. This will add additional insights to the development of a sustainable and effective national AMR surveillance system in Cambodia and other low- and middle-income countries.

Methods

Key informants with a role in governing or contributing data to the laboratory-based surveillance system were interviewed. Emerging themes were identified using the framework analysis method. Laboratories contributing to the AMR surveillance system were assessed on their capacity to conduct quality testing and report data. The laboratory assessment tool (LAT), developed by the World Health Organisation (WHO), was adapted for assessment of a diagnostic microbiology laboratory covering quality management, financial and human resources, data management, microbiology testing performance and surveillance capacity.

Results

Key informants identified inadequate access to laboratory supplies, an unsustainable financing system, limited capacity to collect representative data and a weak workforce to be the main barriers to implementing an effective surveillance system. Consistent engagement between microbiology staff and clinicians were reported to be a key factor in generating more representative data for the surveillance system. The laboratory assessments identified issues with quality assurance and data analysis which may reduce the quality of data being sent to the surveillance system and limit the facility-level utilisation of aggregated data. A weak surveillance network and poor guidance for outbreak response were also identified, which can reduce the laboratories' opportunities in detecting critical or emerging resistance occurring in the community or outside of the hospital's geographical coverage.

Conclusion

This study identified two primary concerns: ensuring a sustainable and quality functioning of microbiology services at public healthcare facilities and overcoming sampling bias at sentinel sites. These issues hinder Cambodia's national AMR surveillance system from generating reliable evidence to incorporate into public health measures or clinical interventions. These findings suggest that more investments need to be made into microbiology diagnostics and to reform current surveillance strategies for enhanced sampling of AMR cases at hospitals.

Blood culture versus antibiotic use for neonatal inpatients in 61 hospitals implementing with the NEST360 Alliance in Kenya, Malawi, Nigeria, and Tanzania: a cross-sectional study

BACKGROUND

Thirty million small and sick newborns worldwide require inpatient care each year. Many receive antibiotics for clinically diagnosed infections without blood cultures, the current 'gold standard' for neonatal infection detection. Low neonatal blood culture use hampers appropriate antibiotic use, fuelling antimicrobial resistance (AMR) which threatens newborn survival. This study analysed the gap between blood culture use and antibiotic prescribing in hospitals implementing with Newborn Essential Solutions and Technologies (NEST360) in Kenya, Malawi, Nigeria, and Tanzania.

METHODS

Inpatient data from every newborn admission record (July 2019-August 2022) were included to describe hospital-level blood culture use and antibiotic prescription. Health Facility Assessment data informed performance categorisation of hospitals into four tiers: (Tier 1) no laboratory, (Tier 2) laboratory but no microbiology, (Tier 3) neonatal blood culture use < 50% of newborns receiving antibiotics, and (Tier 4) neonatal blood culture use > 50%.

RESULTS

A total of 144,146 newborn records from 61 hospitals were analysed. Mean hospital antibiotic prescription was 70% (range = 25-100%), with 6% mean blood culture use (range = 0-56%). Of the 10,575 blood cultures performed, only 24% (95%CI 23-25) had results, with 10% (10-11) positivity. Overall, 40% (24/61) of hospitals performed no blood cultures for newborns. No hospitals were categorised as Tier 1 because all had laboratories. Of Tier 2 hospitals, 87% (20/23) were District hospitals. Most hospitals could do blood cultures (38/61), yet the majority were categorised as Tier 3 (36/61). Only two hospitals performed > 50% blood cultures for newborns on antibiotics (Tier 4).

CONCLUSIONS

The two Tier 4 hospitals, with higher use of blood cultures for newborns, underline potential for higher blood culture coverage in other similar hospitals. Understanding why these hospitals are positive outliers requires more research into local barriers and enablers to performing blood cultures. Tier 3 facilities are missing opportunities for infection detection, and quality improvement strategies in neonatal units could increase coverage rapidly. Tier 2 facilities could close coverage gaps, but further laboratory strengthening is required. Closing this culture gap is doable and a priority for advancing locally-driven antibiotic stewardship programmes, preventing AMR, and reducing infection-related newborn deaths.

A case for routine microbial diagnostics: Results from antimicrobial susceptibility testing in post-traumatic wound infections at a Ugandan tertiary care hospital

The global spread of antimicrobial resistance (AMR) poses an increasing challenge for clinicians in Uganda, where microbiological diagnostics are not routinely available or accessible. The aim of this study was to determine pathogen prevalence and antibiotic resistance patterns in patients with wound infections following trauma at a national referral hospital in Kampala, Uganda. In addition, the suitability of currently used empirical treatment options in this setting was evaluated. This prospective, observational study analysed antimicrobial prescriptions, culture results and antimicrobial sensitivity testing (AST) of wound swabs and blood samples from patients with clinical signs of wound infections on the trauma ward. A total of 124 patients (n = 99, 79.8% male) with a median age of 30 years (IQR 23-39) were enrolled between October 2021 and January 2022. Wound infections were classified as nosocomial in 69% of the cases. Pathogens were isolated from 122 wound swabs, yielding 238 bacterial isolates. The most prevalent pathogens were gram-negative bacteria including Escherichia coli (n = 48, 20.2%) and Acinetobacter spp. (n = 43, 18.1%). Empiric treatment consisted of ceftriaxone and gentamicin which was administered to 67.2% (n = 78) and 62.1% (n = 72) of patients, respectively. High rates of antimicrobial resistance could be demonstrated across gram-negative and gram-positive species towards the most common empiric antibiotics. Following the AST results, over 95% (n = 111) of patients required a change of treatment. Our findings demonstrate that current empiric treatment for wound infections is missing its target in hospitalized patients in Kampala. To address the growing problem of AMR in Uganda, there is a pressing need to enhance diagnostic capacity and implement structured antimicrobial stewardship programs.

Shigellosis in Southeast Asia: A systematic review and meta-analysis

BACKGROUND

Southeast Asia is attractive for tourism. Unfortunately, travelers to this region are at risk of becoming infected with Shigella. We conducted a meta-analysis to provide updates on Shigella prevalence in Southeast Asia, along with their serogroups and serotypes.

METHODS

We conducted a systematic search using PubMed, EMBASE, and Web of Science for peer-reviewed studies from 2000 to November 2022. We selected studies that detected Shigella in stools by culture or polymerase chain reaction (PCR). Two reviewers extracted the data using a standardized form and performed quality assessments using the Joanna Briggs Institute checklist. The random effects model was used to estimate the pooled prevalence of Shigella.

RESULTS

During our search, we identified 4376 studies. 29 studies (from six Southeast Asian countries) were included in the systematic review, 21 each in the meta-analysis of the prevalence of Shigella (Sample size: 109545) and the prevalence of Shigella serogroups. The pooled prevalence of Shigella was 4% (95% CI: 4-5%) among diarrhea cases. Shigella sonnei was the most abundant serogroup in Thailand (74%) and Vietnam (57%), whereas Shigella flexneri was dominant in Indonesia (72%) and Cambodia (71%). Shigella dysenteriae and Shigella boydii were uncommon (pooled prevalence of 1% each). The pooled prevalence of Shigella was 5% (95% CI: 4-6%) in children aged <5 years. The pooled prevalence showed a decreasing trend comparing data collected between 2000-2013 (5%; 95% CI: 4-6%) and between 2014-2022 (3%; 95% CI: 2-4%). Shigella prevalence was 6% in studies that included participants with mixed pathogens versus 3% in those without. Shigella flexneri serotype 2a was the most frequently isolated (33%), followed by 3a (21%), 1b (10%), 2b (3%), and 6 (3%).

CONCLUSIONS

This study provides compelling evidence for the development of effective Shigella vaccines for residents of endemic regions and travellers to these areas.

Evaluation of InTray Cassettes Directly from Blood Cultures for the Diagnosis of Sepsis in Clinical Bacteriology Laboratories as an Alternative to Classic Culture Media

Culture media is fundamental in clinical bacteriology for the detection and isolation of bacterial pathogens. However, in-house media preparation could be challenging in low-resource settings. InTray^® cassettes (Biomed Diagnostics) could be a valid alternative as they are compact, ready-to-use media preparations. In this study, we evaluate the use of two InTray media as a subculture alternative for the diagnosis of bloodstream infections: the InTray^® Müller-Hinton (MH) chocolate and the InTray^® Colorex™ Screen. The InTray MH chocolate was evaluated in 2 steps: firstly, using simulated positive blood cultures (reference evaluation study), and secondly, using positive blood cultures from a routine clinical laboratory (clinical evaluation study). The Colorex Screen was tested using simulated poly-microbial blood cultures. The sensitivity and specificity of the InTray MH chocolate were respectively 99.2% and 90% in the reference evaluation study and 97.1% and 88.2% in the clinical evaluation study. The time to detection (TTD) was ≤20 h in most positive blood cultures (99.8% and 97% in the two studies, respectively). The InTray^® MH Chocolate agar showed good performance when used directly from clinical blood cultures for single bacterial infections. However, mixed flora is more challenging to interpret on this media than on Colorex™ Screen, even for an experienced microbiologist.

Performance of Phenotypic Tests to Detect β-Lactamases in a Population of β-Lactamase Coproducing Enterobacteriaceae Isolates

Objectives This study aimed to evaluate the performance of routinely used phenotypic tests to detect β-lactamase production in isolates coproducing multiple β-lactamase types.

Methods Commonly used phenotypic tests for the detection of extended spectrum β-lactamases (ESBL), AmpC β-lactamase, and carbapenemases were compared with detection and sequencing of β-lactamase genes (as the reference test) in 176 uropathogenic Enterobacteriaceae coproducing multiple β-lactamases from two hospitals in the Western Province of Sri Lanka.

Results Majority of the isolates (147/176, 83.5%) carried β-lactamase genes with (90/147, 61%) harboring multiple genes. The Clinical and Laboratory Standards Institute screening method using cefotaxime (sensitivity [Se], 97; specificity [Sp], 93; accuracy [Ac], 94) and ceftriaxone (Se, 97; Sp, 91; Ac, 93) was the most effective to detect ESBLs. The modified double disc synergy test (Se, 98; Sp, 98; Ac, 97) and combined disc test (Se, 94; Sp, 98; Ac, 96) showed good specificity for confirmation of ESBLs. Cefoxitin resistance (Se, 97; Sp, 73; Ac, 85) and the AmpC disc test (Se, 96; Sp, 82; Ac, 86) were sensitive to detect AmpC β-lactamase producers coproducing other β-lactamases but showed low specificity, probably due to coproduction of carbapenemases. Meropenem was useful to screen for New Delhi metallo β-lactamases and OXA-48-like carbapenemases (Se, 97; Sp, 96; Ac, 96). The modified carbapenem inactivation method showed excellent performance (Se, 97; Sp, 98; Ac, 97) in identifying production of both types of carbapenemases and was able to distinguish this from carbapenem resistance due to potential mutations in the porin gene.

Conclusions Microbiology laboratories that are still depend on phenotypic tests should utilize tests that are compatible with the types of β-lactamase prevalent in the region and those that are least affected by coexisting resistance mechanisms.