The analysis, covering publications from 2000 to 2025, drew on the Scopus database and followed a PRISMA-adapted screening workflow to construct a final analytical corpus of 1,746 articles and reviews spanning 432 journals and involving 11,277 unique authors. The field has expanded at a compound annual growth rate of 17.10%, accumulating 42,075 citations with an average of 24.10 citations per document. Growth accelerated sharply after 2018: annual output rose from 84 publications in 2018 to 259 in 2025, a trajectory the study attributes to increasing prioritization of antimicrobial resistance on the global research agenda and a post-pandemic surge in translational diagnostic research.

To frame the analysis, the study anchored itself in the World Health Organization’s bacterial priority pathogen lists. The WHO’s 2017 framework classified resistant bacteria into critical, high, and medium priority categories, and its 2024 update expanded the list to 24 pathogens across 15 bacterial families using multicriteria decision analysis that weighed mortality, incidence, resistance trends, transmissibility, preventability, treatability, and the state of the drug development pipeline. The critical tier now includes carbapenem-resistant Acinetobacter baumannii, carbapenem-resistant and third-generation cephalosporin-resistant Enterobacterales, and rifampicin-resistant Mycobacterium tuberculosis, while carbapenem-resistant Pseudomonas aeruginosa was moved from critical to high priority based on regional resistance trends and comparatively lower transmission capacity.

Against this backdrop, the bibliometric results reveal a field organized around distinct pathogen axes. Staphylococcus aureus dominated the corpus with 730 publications and 21,945 total citations, followed by Mycobacterium tuberculosis with 439 publications, Enterobacterales with 389, Pseudomonas aeruginosa with 309, Acinetobacter baumannii with 279, and Enterococcus faecium with 250. Growth over the past five years was strongest for Streptococcus pneumoniae at 27.79%, Pseudomonas aeruginosa at 26.35%, and Enterobacterales at 22.81%, signaling a decisive shift in research attention toward Gram-negative carbapenem resistance as the most urgent clinical frontier.

At the platform level, conventional PCR and nucleic acid amplification testing appeared in 61.51% of publications, while whole-genome sequencing featured in 55.44%, making these two technologies the twin pillars of the literature. Because platform categories were not mutually exclusive, many publications combined both approaches. Multiplex PCR stood out for impact, averaging 42.57 citations per article, reflecting the foundational role of early target-specific resistance detection. Emerging technologies, including nanopore sequencing, metagenomic sequencing, and CRISPR-based diagnostics, appeared at low frequencies but formed distinct and growing clusters, suggesting they represent innovation fronts that have not yet reached routine clinical integration.

Resistance marker analysis identified mecA/mecC, rpoB, blaNDM, katG, and vanA/vanB as the most frequently studied molecular targets. Methicillin resistance in staphylococci, epitomized by the mecA gene and its newer variant mecC, anchored the Gram-positive research tradition, while the tuberculosis markers rpoB, katG, and inhA defined a mature and specialized diagnostic axis. Carbapenemase genes, including blaKPC, blaNDM, and blaOXA-48, together with the mobile colistin resistance gene mcr and the fluoroquinolone targets gyrA and parC, showed the strongest recent growth, with gyrA and parC expanding at compound annual rates of 44.28% and 49.53% respectively over the last five years.

Thematic mapping of keyword co-occurrence networks revealed that the literature is structured around six interpretable clusters. Two emerged as mature core themes: PCR-based rapid antimicrobial resistance detection, organized around MRSA, multiplex PCR, and the mecA/mecC and vanA/vanB markers, and a whole-genome sequencing and genomic epidemiology theme spanning multiple pathogen groups. The tuberculosis resistance marker axis formed a strong but specialized mature theme, while the carbapenemase and Gram-negative resistance gene cluster, the metagenomic and nanopore clinical diagnostics cluster, and a general cross-pathogen antimicrobial resistance cluster were identified as emerging or niche research fronts.

Thematic evolution analysis across three time windows documented a clear conceptual restructuring. The early period from 2000 to 2010 centered on target-specific markers such as mecA, vancomycin resistance, and real-time PCR, reflecting an era of single-gene rapid tests. The middle period from 2011 to 2020 brought whole-genome sequencing, tuberculosis, multiplex PCR, and the Enterobacterales-carbapenemase axis to prominence. The recent period from 2021 to 2025 represents a more integrated antimicrobial resistance framework in which WGS, Staphylococcus aureus, and antibiotic resistance concepts dominate, demonstrating the field’s transition from individual marker detection to genomically integrated, translationally oriented diagnostics.

The study’s methodological rigor included a validation exercise in which 150 randomly selected records were blindly reassessed to test the rule-based text-matching system used to classify pathogens, platforms, markers, and clinical contexts. Concordance rates reached 100% for platform and resistance-marker labels, 91.3% for pathogen labels, and 86.7% for clinical-context labels, yielding an overall average agreement of 94.5%. The analysis also mapped the geography of the field: China led production with 263 publications, followed by the United States with 252, the United Kingdom with 130, and Germany with 127, though the United Kingdom and France showed higher rates of international collaboration and network centrality, revealing a divide between volume-based productivity and collaboration-intensive influence.

The findings carry important implications for clinical practice. Prior evidence shows that rapid diagnostic tests, when deployed alongside antimicrobial stewardship programs, reduce mortality in bloodstream infections compared with blood culture alone. The bibliometric structure documented here confirms that molecular diagnostics has evolved beyond answering whether a pathogen is present, into a multilayered data-generating enterprise that supports resistance prediction, monitoring of clonal spread, and clinical and public health decision-making. At the same time, the study acknowledges limitations: PCR panels and WGS report genetic content rather than physiological state, meaning phenomena such as bacterial persistence and tolerance fall largely outside the field’s marker-centered vocabulary, and future work integrating phenotypic, genomic, and virulence-layer data will be essential to close the gap between resistance prediction and treatment outcome.

Subject of Research: Bibliometric mapping of molecular diagnostic platforms and resistance markers for WHO priority bacterial pathogens

Article Title: Molecular Diagnostics for WHO Priority Bacterial Pathogens: A Bibliometric Mapping of Diagnostic Platforms, Resistance Markers, and Antimicrobial Resistance Research Trends

Article References: Ünlü, S. (2026). Molecular Diagnostics for WHO Priority Bacterial Pathogens: A Bibliometric Mapping of Diagnostic Platforms, Resistance Markers, and Antimicrobial Resistance Research Trends. MicrobiologyOpen, 15(5), Article e70394. https://doi.org/10.1002/mbo3.70394

Image Credits: AI Generated

DOI: 10.1002/mbo3.70394

Keywords: antimicrobial resistance, molecular diagnostics, WHO priority pathogens, whole-genome sequencing, PCR, bibliometric analysis, MRSA, carbapenemase genes, Mycobacterium tuberculosis, Enterobacterales, CRISPR diagnostics, genomic epidemiology

The research, led by Tizazu Zelelie, Biniam Mekonnen, and Demiss Nigussie and published in Public Health in Practice, was designed around the One Health framework, the internationally endorsed recognition that human, animal, and environmental health are inseparable. First formalized in 2015 by the tripartite coalition of the Food and Agriculture Organization, the World Health Organization, and the World Organization for Animal Health, and later expanded to include the United Nations Environment Programme, the approach acknowledges that resistant bacteria and their genes do not respect the boundaries between hospital wards, farms, and waterways. Resistant organisms shed into the environment can transfer their resistance genes horizontally to other bacteria infecting humans and animals, creating reservoirs of resistance that no single-sector intervention can drain. East Africa presents particularly fertile ground for this dynamic, combining agricultural and pastoral livelihoods with patterns of antimicrobial misuse, limited access to clean water, poor sanitation, and inadequate infection prevention infrastructure.

To capture the full scope of the problem, the authors searched PubMed, ScienceDirect, and Google Scholar for studies reporting carbapenem-resistant E. coli isolated from humans, animals, food, or the environment in thirteen East African countries. Following the PRISMA reporting guidelines and registered prospectively on PROSPERO, the review screened more than 4,300 records, ultimately retaining twenty-nine studies that met rigorous eligibility criteria. Each study was assessed for bias by two independent reviewers using the Newcastle Ottawa Scale, and all were judged to carry low risk of bias, scoring at or above the six-star threshold. The researchers then performed a random-effects meta-analysis using restricted maximum likelihood estimation in the R statistical environment, quantifying heterogeneity with the I-squared statistic and probing publication bias with funnel plots and Egger’s test.

The numbers underlying the headline finding are substantial. Across the included studies, the combined sample size reached 11,581 participants and specimens, from which 3,908 E. coli isolates were recovered. Of those, 442 strains proved resistant to carbapenem antibiotics. The studies were heavily weighted toward clinical settings, with seventy-six percent hospital-based and human samples accounting for nearly eighty percent of all sources, but the remainder drew from environmental reservoirs, food, and animals, giving the analysis its distinctive cross-sector character. Geographically, Ethiopia dominated the evidence base with fourteen studies, followed by Uganda with seven, Sudan with four, Tanzania with two, and single studies from Djibouti and Kenya. No eligible studies emerged from the other seven countries in the region, itself a telling indicator of surveillance gaps.

Beneath the pooled estimate of 12.7 percent lies a sobering spread. The lowest reported prevalence was 0.5 percent in an Ethiopian study, while the highest, drawn from sewage at a Ugandan referral hospital, reached a remarkable 50 percent. In subgroup analyses, Sudan recorded the highest country-level pooled prevalence at 24.7 percent, followed by Uganda at 17.4 percent and Ethiopia at 9.9 percent. More striking still was the finding that the environment emerged as the most contaminated interface of all, with a pooled prevalence of 24.2 percent among environmental isolates, compared with 11.9 percent in humans, 7.7 percent in food, and 4.2 percent in animals. Clinical samples of multiple types yielded a pooled prevalence of 15.8 percent. These figures suggest that hospitals, farms, and communities are continuously seeding the environment with resistant organisms, which in turn serve as a reservoir capable of reinfecting the human population.

Genetic analysis revealed the molecular arsenal behind this resistance. Half of the included studies, 51.7 percent, reported the detection of carbapenemase-encoding genes, including KPC and GES from the class A serine beta-lactamases, NDM-1 and NDM-5, VIM, IMP, and SPM among the metallo-beta-lactamases, and OXA-48 and OXA-181 oxacillinases. These genes encode enzymes that destroy carbapenems and are readily transferred between bacterial species on mobile genetic elements, meaning a resistance trait that emerges in one organism can rapidly colonize others. The World Health Organization ranks carbapenem-resistant pathogens first on its global priority list of antibiotic-resistant bacteria precisely because treatment options for them are so desperately limited: essentially reduced to polymyxins, fosfomycin, and tigecycline, older or more toxic drugs that represent imperfect substitutes for an entire antibiotic class.

The stakes of this trend are measured in lives. Global modeling published in the Lancet estimates that bacterial antimicrobial resistance was associated with nearly 5 million deaths in 2021, contributing to roughly one in eight deaths worldwide, and projects that as many as 8.22 million deaths annually could be attributable to AMR by 2050 if current trajectories continue. In the WHO African region alone, more than one million deaths were associated with resistant bacteria in 2019. Among Gram-negative bacteria, resistance to carbapenems has climbed faster than to any other antibiotic class, with associated deaths rising from 619,000 in 1990 to 1.03 million in 2021. Carbapenem-resistant Enterobacteriaceae infections are linked to longer hospital stays, higher healthcare costs, and elevated mortality, burdens that fall hardest on health systems with the least capacity to absorb them.

The review also captured a subtle temporal signal. Prevalence in studies published between 2021 and 2025 was marginally lower, at 12.6 percent, than in the 2015 to 2020 window, which averaged 13.5 percent, though the authors note this difference was not statistically significant and may simply reflect variation in study designs, settings, and target populations. Regional trend data from Ethiopia’s Amhara Public Health Institute, which showed resistance climbing to a peak in 2019 before declining, offers tentative grounds for the hope that sustained interventions can bend the curve. At the same time, the extraordinarily high statistical heterogeneity among the studies, with an I-squared value of 93.3 percent, underscores how differently the epidemic of resistance is unfolding across countries, populations, and sample types, and the authors caution that significant publication bias was detected and statistically adjusted in their estimates.

Perhaps the most consequential implication of the study is what it says about surveillance and regional coordination. The authors attribute the region’s elevated burden to weak laboratory capacity, poor health system governance, limited diagnostic infrastructure, and the destabilizing effects of conflict in countries such as Sudan and Ethiopia, all compounded by prolonged and often inappropriate antimicrobial use in both human and animal populations. Because routine testing for carbapenemase production is rarely performed in African clinical laboratories, the true prevalence may well exceed what published studies capture. The authors call for effective implementation of the One Health approach across sectors, strengthened routine diagnostic capacity, national and regional surveillance programs, rapid detection methods, and integration that extends beyond health policy alone. Without such coordinated action, the environmental reservoirs documented at prevalence rates approaching one in four isolates will continue to replenish the human burden, ensuring that one of medicine’s final antibiotics loses its power across one of the world’s most vulnerable regions.

Subject of Research: Prevalence and molecular epidemiology of carbapenem-resistant E. coli across human, animal, and environmental interfaces in East Africa

Article Title: Carbapenem-resistant E. coli with one-health approach in East Africa: Systematic review and meta-analysis

Article References: Zelelie, T., Mekonnen, B., & Nigussie, D. (2026). Carbapenem-resistant E. coli with one-health approach in East Africa: Systematic review and meta-analysis. Public Health in Practice, 12, Article 100843. https://doi.org/10.1016/j.puhip.2026.100843

Image Credits: AI Generated

DOI: 10.1016/j.puhip.2026.100843

Keywords: carbapenem-resistant E. coli, antimicrobial resistance, One Health, East Africa, systematic review, meta-analysis, carbapenemase genes, NDM, public health surveillance, Ethiopia, Uganda, Sudan

Carbapenem-resistant Enterobacterales, commonly abbreviated CRE, represent one of the most urgent threats in modern medicine. These Gram-negative bacteria, which include Escherichia coli and Klebsiella pneumoniae among others, have acquired the ability to withstand carbapenems, a class of antibiotics often reserved as a last line of defense against serious infections. The consequences are stark: mortality rates from CRE infections can climb as high as fifty percent, leaving clinicians with vanishingly few therapeutic options. The problem is also accelerating globally, with resistance prevalence rising from just one percent in 2013 to forty-three percent in 2020 in parts of North America, a trajectory that underscores how quickly these organisms can adapt and spread.

The engine driving this resistance is the production of carbapenemase enzymes, a diverse family of beta-lactamases grouped into distinct classes by the Ambler classification system. Class A enzymes such as KPC, Class B metallo-beta-lactamases including NDM, IMP and VIM, and Class D oxacillinases such as OXA-48 each hydrolyze carbapenems through different chemical mechanisms. Because phenotypic tests alone cannot reliably distinguish between these classes, molecular techniques such as multiplex polymerase chain reaction are essential for pinpointing which resistance genes are actually present. In the Indian context, where blaNDM-1 has become widespread, identifying these determinants is critical for predicting transmissibility, constructing empirical antibiograms and strengthening hospital infection control.

Recognizing that systematic molecular data from eastern India were virtually absent, the AIIMS Patna team designed a cross-sectional study conducted between July 2021 and July 2023 in the hospital’s Microbiology laboratory. The research, approved by the Institutional Ethics Committee under approval number AIIMS/Pat/IEC/2021/578 and performed in accordance with the Declaration of Helsinki, analyzed residual clinical isolates collected during routine diagnostic work, with a formal waiver of individual patient consent and no patient-identifiable data collected. To avoid duplication bias, the investigators included only the first isolate per patient per episode of infection, ensuring that repeated cultures from the same admission did not inflate the results.

The scope of the underlying resistance problem was formidable. During the study period, a total of 3,421 Enterobacterales were isolated, drawn overwhelmingly from urine specimens, followed by pus, blood and respiratory samples. Of these, 1,128 isolates, or 32.97 percent, were phenotypically confirmed as carbapenem resistant, a figure drawn from the team’s previously published phenotypic work at the same center. Resistance was markedly higher among inpatients, at 47.74 percent, compared with only 14.48 percent among outpatients. All 213 CRE isolates characterized in detail showed complete resistance to third-generation cephalosporins, near-universal resistance of 99.4 percent to beta-lactam and beta-lactamase inhibitor combinations such as piperacillin-tazobactam, and one hundred percent resistance to aztreonam, a sobering profile that leaves almost no conventional beta-lactam therapy intact.

To confirm which isolates were producing carbapenemase enzymes, the researchers deployed a battery of phenotypic assays, including the Modified Carbapenem Inactivation Method, or mCIM, its EDTA-supplemented variant eCIM designed to identify Class B metallo-beta-lactamases, and combination inhibition tests using phenylboronic acid, cloxacillin and EDTA. Of the 213 CRE isolates, 203 were confirmed carbapenemase producers by mCIM. From this positive pool, a consecutive subset of 98 isolates with viable stored stock and sufficient DNA yield was selected for multiplex PCR-based gene profiling using validated primers originally described by Poirel and colleagues, with amplification performed on a ProFlex thermocycler and amplicons resolved on agarose gels. The authors caution that all gene-detection rates apply to this genotyped subset, which represents 48.3 percent of the mCIM-positive isolates, and should not be extrapolated as prevalence estimates for the entire CRE cohort.

The molecular results were striking. Among the 98 profiled isolates, 60 were Escherichia coli, 33 were Klebsiella pneumoniae, and the remainder comprised Citrobacter freundii and Enterobacter species. blaNDM emerged as the most prevalent gene, detected in 63.27 percent of isolates, with E. coli and K. pneumoniae as the predominant carriers. blaOXA-48 followed closely at 61.22 percent, while blaIMP appeared in 10.20 percent, blaKPC in 5.10 percent and blaVIM in 3.06 percent. Perhaps most concerning was the degree of co-carriage: half of the genotyped K. pneumoniae isolates carried both NDM and OXA-48 simultaneously, and 27.27 percent of E. coli harbored the same dual combination. Individual isolates carrying three resistance genes, such as NDM, OXA-48 and KPC together, were also documented, illustrating how bacterial genomes can accumulate layered defensive armories.

The comparison between phenotypic and genotypic results revealed both reassuring agreement and instructive discrepancies. All isolates carrying blaKPC were mCIM positive and displayed Class A carbapenemase phenotypes, and every isolate harboring a metallo-beta-lactamase gene, whether blaNDM, blaIMP or blaVIM, was positive on both mCIM and eCIM, confirming Class B enzyme production. However, among the 60 isolates carrying blaOXA-48, only two exhibited the phenotypic signature of Class D carbapenemase, a gap the authors attribute partly to limitations in the EUCAST-recommended temocillin zone-diameter threshold used as an indirect confirmatory test. Unexpressed genes, undetected beta-lactamase families such as blaSPM or blaGIM, and PCR inhibitors may all contribute to such mismatches, and the researchers note that amplicons were not confirmed by sequencing, meaning allelic variants cannot be entirely excluded.

These findings carry direct implications for therapy. Given the overwhelming predominance of Class B metallo-beta-lactamases, particularly NDM, the authors argue that empirical treatment of suspected CRE infections in this region should prioritize agents with proven activity against Class B enzymes, such as cefiderocol or the combination of ceftazidime-avibactam with aztreonam. They also emphasize that neither phenotypic nor genotypic testing alone is sufficient, and that balancing both approaches offers the most complete picture of resistance. International comparisons in the study highlight how sharply gene distributions vary by geography, with Thailand reporting NDM rates of ninety percent, China dominated by KPC at 53.4 percent, and Saudi Arabia led by OXA-48 at 76.11 percent, reinforcing that local surveillance data are indispensable for guiding rational antibiotic use.

Beyond its immediate clinical relevance, the study fills a critical gap in India’s national antimicrobial resistance surveillance architecture. Bihar and neighboring eastern states carry enormous infectious disease burdens yet have historically lacked the molecular diagnostic capacity to characterize circulating resistance mechanisms, undermining targeted infection control interventions. By documenting the genotypic landscape of CRE in an underrepresented setting, the AIIMS Patna team supports the objectives of India’s National Action Plan on Antimicrobial Resistance, particularly those concerning laboratory strengthening and evidence-based surveillance. The researchers acknowledge limitations, including the subset-based genotyping design and the absence of sequencing-based strain typing, and they plan future work involving blaNDM allele subtyping and whole-genome sequencing to trace clonal spread. For now, their findings stand as a clear warning and a practical guide: the superbugs of eastern India are armed with a dangerous genetic repertoire, but knowing exactly which weapons they carry is the first step toward disarming them.

Subject of Research: Genotypic profiling of carbapenemase genes in carbapenem-resistant Enterobacterales at a tertiary care hospital in Bihar, India

Article Title: Deciphering the genotypic profiles of Carbapenem-resistant Enterobacterales: A study from a tertiary care hospital in Bihar, India

Article References: Pramurtajyoti, D., Prathyusha, K., Zeeshan, F. M., Asim, S., Pati Binod, K., & Bhaskar, T. (2026). Deciphering the genotypic profiles of Carbapenem-resistant Enterobacterales: A study from a tertiary care hospital in Bihar, India. New Microbes and New Infections, 73, Article 101850. https://doi.org/10.1016/j.nmni.2026.101850

Image Credits: AI Generated

DOI: 10.1016/j.nmni.2026.101850

Keywords: carbapenem-resistant Enterobacterales, antimicrobial resistance, blaNDM, blaOXA-48, carbapenemase genes, multiplex PCR, Klebsiella pneumoniae, Escherichia coli, metallobeta-lactamases, India, hospital surveillance, infection control