Hospital study finds bacteria carrying both last-resort resistance genes spreading in wards

In a tertiary care hospital in Northeast India, researchers spent seven years collecting samples from patients with soft tissue infections, and what they found offers a sobering snapshot of how drug-resistant bacteria are quietly evolving inside hospitals. Between 2019 and 2025, a team from the Department of Microbiology at AGMC & GBP Hospital in Agartala screened 3,133 samples from superficial and deep tissue infections and recovered 351 isolates of non-fermenting Gram-negative bacilli, a group of opportunistic pathogens that includes some of the most feared hospital-acquired organisms in modern medicine. The study, published in Molecular Biology Reports, combined phenotypic testing, polymerase chain reaction based gene detection, and genomic fingerprinting to map exactly which resistance determinants these bacteria carry and how they are spreading from patient to patient.

Non-fermenting Gram-negative bacilli, abbreviated NFGNB, are a heterogeneous group of bacteria that do not ferment glucose and thrive in moist hospital environments. The two most clinically important members are Pseudomonas aeruginosa and the Acinetobacter calcoaceticus-baumannii complex, both of which have climbed the World Health Organization’s priority lists for antibiotic research because they increasingly shrug off nearly every drug in the formulary. In the Agartala cohort, Pseudomonas aeruginosa dominated, accounting for 88.3 percent of the isolates, while the Acinetobacter calcoaceticus-baumannii complex made up the remaining 11.7 percent. Soft tissue infections, which range from superficial wound infections to deep, life-threatening involvement of fascia and muscle, represent a particularly dangerous niche for these organisms because damaged tissue provides an entry point and local blood supply may be compromised.

The central therapeutic problem examined in the study is the loss of two critical drug classes. Carbapenems, once considered the reliable last line of defense against Gram-negative infections, are rendered ineffective when bacteria produce metallo-beta-lactamases, or MBLs, enzymes that use a zinc ion at their active site to hydrolyze the beta-lactam ring common to penicillins, cephalosporins, and carbapenems alike. When carbapenems fail, clinicians often turn to colistin, a polymyxin antibiotic so toxic to the kidneys that it was largely abandoned in the 1970s and then revived as a drug of last resort. Colistin resistance, in turn, can be mediated by mcr genes, mobile genetic elements that modify the lipopolysaccharide of the bacterial outer membrane so that the drug can no longer bind. The prospect of bacteria carrying both mechanisms simultaneously is what keeps infection control specialists awake at night, because it effectively removes the final pharmacological safety net.

To quantify the scale of the problem, the researchers first used the combined disk test, a phenotypic assay in which carbapenem disks are placed on bacterial lawns with and without a chelating agent such as EDTA that strips zinc from metallo-beta-lactamases. If the inhibition zone around the disk expands in the presence of the chelator, the enzyme is identified as an MBL. This screening identified MBL production in 25 of the Pseudomonas aeruginosa isolates and 13 of the Acinetobacter calcoaceticus-baumannii complex isolates. The team then confirmed and characterized the resistance at the molecular level using PCR to detect three major MBL gene families: blaNDM, blaIMP, and blaVIM. Among the isolates carrying MBL genes, blaNDM, which encodes the New Delhi metallo-beta-lactamase, was clearly predominant, consistent with the gene’s well-documented dominance across the Indian subcontinent and its global dissemination through travel and medical tourism.

On the colistin front, the picture was equally concerning. Resistance to colistin was observed in 19.5 percent of the Acinetobacter calcoaceticus-baumannii complex isolates, a substantial proportion given that colistin is frequently the only remaining option for these infections. The researchers screened for the full panel of known mobile colistin resistance genes, mcr-1 through mcr-9, using PCR. The most alarming finding was the detection of two strains harboring both blaNDM and mcr-3 simultaneously, meaning these bacteria could destroy carbapenems with a metallo-enzyme and block colistin binding with an MCR-3 modified cell surface. The mcr-3 gene is particularly interesting from an evolutionary standpoint because, unlike the more widely studied mcr-1 which originated in Escherichia coli from livestock, mcr-3 has been documented in diverse bacterial species and environments, and recent work has suggested that the MCR-3 enzyme may even help bacteria evade host phagocytosis, adding a virulence dimension to its resistance role.

Detecting resistance genes is only half the story; understanding how resistant strains move through a hospital is equally important for stopping them. For this, the team turned to ERIC-PCR, enterobacterial repetitive intergenic consensus polymerase chain reaction, a genomic fingerprinting technique that amplifies DNA regions between repetitive elements scattered across bacterial chromosomes. Because the spacing and number of these elements vary between strains, the resulting banding patterns serve as a rapid, low-cost proxy for genetic relatedness. The researchers analyzed the banding profiles using GelJ software and constructed phylogenetic trees with MEGA11 to visualize which isolates were likely clonal descendants of a common ancestor.

The fingerprinting results revealed clonal dissemination within the hospital, with genetically related isolates clustering particularly in the surgery and burn wards. This is epidemiologically significant because burn patients and surgical patients share predictable risk factors: breached skin barriers, prolonged hospital stays, indwelling devices, and heavy exposure to broad-spectrum antibiotics that select for resistant organisms. When a single clone establishes itself in such a ward, standard cleaning and hand hygiene failures allow it to colonize successive patients. Notably, the clustered isolates mostly shared cluster-specific resistance patterns, meaning that members of the same genetic lineage carried the same resistance gene profile. This concordance between genotype and resistance phenotype suggests that resistance determinants are being inherited vertically along with the clone itself rather than acquired independently by unrelated strains, which strengthens the case that transmission of whole organisms, not just horizontal gene transfer, is driving the observed pattern.

The co-occurrence of blaNDM and mcr-3 in the same strains deserves particular emphasis because it represents a convergence of two resistance mechanisms that were historically carried by different bacterial populations in different reservoirs. Carbapenem resistance has long been entrenched in hospital settings, while mcr genes were first identified in food animals and agricultural environments, raising fears that the agricultural and clinical reservoirs would eventually merge. The Agartala findings provide direct evidence that this convergence is happening in clinical isolates from soft tissue infections, not merely in surveillance studies of gut carriage. Each additional resistance mechanism stacked onto a circulating clone narrows the therapeutic window further; an infection caused by a strain producing NDM and carrying mcr-3 leaves clinicians with very few options, potentially including older, more toxic agents or combination therapies with limited evidence behind them.

The authors of the study, Ankan Chakrabarti, Tapan Majumdar, and Sibabrata Bhattacharya, frame their findings as a call for continuous molecular surveillance, rigorous hospital infection control, and stringent antibiotic stewardship. The seven-year prospective design strengthens the conclusions because it captures trends across time rather than a single snapshot, and the combination of phenotypic, molecular, and typing methods provides a layered picture of the resistance problem. The study was conducted with ethical approval from the institutional ethics committee and informed consent from participants, and the authors report no competing interests. While the data come from a single tertiary care center in Northeast India, the mechanisms documented there are not geographically confined; blaNDM and mcr genes travel readily through plasmids, transposons, and the international movement of patients.

For the broader scientific and public health community, the study underscores several practical lessons. First, soft tissue infections should not be overlooked as a reservoir of extreme drug resistance, since much surveillance attention focuses on bloodstream and respiratory isolates. Second, genotyping methods such as ERIC-PCR, despite being older and less granular than whole-genome sequencing, remain valuable tools for resource-limited laboratories to detect outbreaks early and trace transmission routes between wards. Third, the detection of mcr genes in Acinetobacter, an organism in which colistin resistance has more often been attributed to chromosomal mutations than to mobile genes, signals that mobile colistin resistance is expanding its host range among non-fermenting bacilli. As hospitals worldwide grapple with the post-antibiotic era, studies like this one from Agartala serve as an early warning: the bacteria that cause the most difficult infections are accumulating resistance determinants faster than new drugs are arriving, and the window for containment through surveillance, hygiene, and disciplined antibiotic use is narrowing with each clonal cluster identified.

Subject of Research: Genomic characterization of metallo-beta-lactamase and mcr-mediated resistance in non-fermenting Gram-negative bacilli from soft tissue infections

Article Title: Genomic characterization of non-fermenting gram-negative bacilli with metallo beta lactamase production and mcr based colistin resistance causing soft tissue infections: a seven-year hospital based prospective cross-sectional study

Article References: Chakrabarti, A., Majumdar, T., & Bhattacharya, S. (2026). Genomic characterization of non-fermenting gram-negative bacilli with metallo beta lactamase production and mcr based colistin resistance causing soft tissue infections: a seven-year hospital based prospective cross-sectional study. Molecular Biology Reports, 53(1), Article 1629. https://doi.org/10.1007/s11033-026-12802-x

Image Credits: AI Generated

DOI: 10.1007/s11033-026-12802-x

Keywords: antimicrobial resistance, metallo-beta-lactamase, NDM, mcr genes, colistin resistance, Pseudomonas aeruginosa, Acinetobacter baumannii, soft tissue infections, ERIC-PCR, nosocomial infection, carbapenem resistance, hospital surveillance