The research, published in Frontiers in Antibiotics by Tristan Lüdecke and Klaus-Peter Hunfeld of the Institute for Laboratory Medicine, Microbiology and Infection Control at Northwest Medical Center in Frankfurt am Main, evaluated the Bruker IR Biotyper as a first-line surveillance typing tool for Serratia isolates recovered from clinical materials. The team compared the FTIR results against whole genome sequencing coupled with bioinformatic analysis, the current gold standard for determining the phylogenetic relationships of clinical isolates. Their findings indicate that, although with some limitations, the infrared approach may serve as a rapid and cost-effective screening method when an outbreak is suspected.

Serratia marcescens, the type strain of the genus, is a facultative human pathogen of the order Enterobacterales that is encountered primarily as a cause of nosocomial infections, particularly in neonatal intensive care units, with sink drains identified as one of the main reservoirs. The bacterium can colonize a wide range of wet surfaces, from artificial nails to medical equipment, vials, the human gastrointestinal and respiratory tract, and materials such as lotions, antiseptics, and even quaternary ammonium-based disinfectants when handled incorrectly. Multi-year-long outbreaks as well as nationwide clonal spreading of Serratia species have been reported, underlining the significance of this facultative pathogen in healthcare settings.

According to the World Health Organization, the rate of nosocomial infections among hospitalized patients in the developed world stands at 7.6 percent, rising to 30 percent in intensive care units. Beyond the risk of increased mortality, these infections prolong hospital stays and drive up antibiotic use and healthcare costs. Although Serratia marcescens accounts for only one to two percent of nosocomial infections, an epidemiological increase in the isolation of Serratia species should prompt further epidemiological workup. The bacterium can carry beta-lactamases such as AmpC, ESBL, and carbapenemases including NDM and KPC, which can render a range of antibiotics ineffective and complicate empirical treatment.

The study was triggered by a six-week period of increased Serratia incidence between February and March 2024 among adult ventilated patients treated in a neurological intensive care unit at a collaborating clinical center. The researchers collected 28 isolates from routine clinical and environmental hygiene samples, including 24 first isolates from respiratory materials such as tracheal secretions, bronchoalveolar lavage, and pharyngeal swabs, a pair of environmental isolates, and two epidemiologically unrelated reference isolates from other institutions. All isolates displayed Serratia-typical antimicrobial susceptibility patterns, including some AmpC beta-lactamase overexpression, but no evidence of multidrug resistance.

Technically, the FTIR workflow was performed with the IR Biotyper using standard manufacturer settings. Isolates were subcultured on Columbia agar with five percent sheep blood, suspended in ethanol and distilled water, and applied to silicon target plates in five technical replicates each. Spectra were acquired in a wave number range of 800 to 1300 inverse centimeters, a region that tends to show the best classification performance. The software applied baseline corrections, smoothing, normalization, second derivative calculation, and vector normalization before hierarchical cluster analysis using the UPGMA algorithm generated dendrograms from which clusters were derived.

The genomic reference work was equally rigorous. DNA was extracted, purified, and sequenced on an Illumina NovaSeq X+ platform with a 2×150 bp paired-end workflow. Core genome multilocus sequence typing was performed using a Serratia marcescens cgMLST scheme comprising 2,692 alleles, with isolates differing by twelve or fewer alleles considered closely related. Pairwise SNP distances within clusters ranged from zero to three in four of the five genomic clusters, confirming clonal relationships, while the two environmental isolates from the same hospital sink differed by 30 SNPs yet were still considered epidemiologically linked because they came from the drain and trap of the same sink.

The species-level results were striking in themselves. While routine biochemical testing and MALDI-TOF mass spectrometry reported Serratia marcescens for all or most isolates, genome-based analysis using Mash Screen, average nucleotide identity, and the type strain genome server revealed a heterogeneous collection spanning Serratia ureilytica, S. bockelmannii, S. sarumanii, S. marcescens, and Serratia nevei, along with a potentially new Serratia species now under investigation. This underscores a known weakness of MALDI-TOF, whose mass spectra are too similar among Serratia species and whose databases do not yet include all recently discovered species.

Performance-wise, the comparison produced a positive predictive value of 0.842 for correctly identifying closely related isolates and a negative predictive value of 1.0 for correctly identifying unrelated ones. FTIR achieved a sensitivity of 1.0, meaning not a single closely related isolate was deemed unrelated, while specificity stood at 0.667, with three unrelated isolates falsely assigned to a cluster. Overall accuracy was 0.88. Concordance with the genomic reference, measured using the Adjusted Rand index and the Adjusted Wallace coefficient, yielded an AR of 0.742, a WGS-to-FTIR AW of 1.0, and an FTIR-to-WGS AW of 0.590, meeting previously suggested criteria for a first-line screening test. The FTIR results also compared favorably with a recent meta-analysis reporting an overall accuracy of 78 percent for Enterobacterales.

The authors caution that their strain collection, the largest set of Serratia isolates comprehensively studied with FTIR to date, came from a single medical center under a suspected outbreak situation, which implies a higher pretest probability of relatedness than a randomly collected set. The small sample size is reflected in wide 95 percent confidence intervals, and FTIR’s reliance on phenotypic traits rather than genetic similarity means wrong clustering events can occur. Strict adherence to standardized culture conditions, incubation times, and sample preparation protocols remains essential. Future research should address larger isolate sets from different locations, single-species sub-analyses, inter-laboratory ring trials, alternative spectral windows, and AI-based raw data analysis. Nevertheless, the study builds a case that infrared fingerprinting could become a complementary analytical addition to the arsenal of clinical microbiology laboratories, enabling the early, focused implementation of infection control countermeasures when every hour counts.

Subject of Research: Microbiology and Infectious Disease

Article Title: Evaluation of Fourier transform infrared spectroscopy as a first-line surveillance typing tool for Serratia spp. isolates derived from clinical materials

Article References: Lüdecke, T., & Hunfeld, K.-P. (2026). Evaluation of Fourier transform infrared spectroscopy as a first-line surveillance typing tool for Serratia spp. isolates derived from clinical materials. Frontiers in Antibiotics, 5, Article 1781370. https://doi.org/10.3389/frabi.2026.1781370

Image Credits: AI Generated

DOI: 10.3389/frabi.2026.1781370

Keywords: FTIR spectroscopy, IR Biotyper, Serratia, whole genome sequencing, nosocomial outbreaks, strain typing, clinical microbiology, infection control, cgMLST, hospital epidemiology, MALDI-TOF, surveillance

The research team, led by Mmabatho Mashapo and Thendo Mafuna of the University of Johannesburg together with colleagues at the University of South Africa and the Agricultural Research Council’s Onderstepoort Veterinary Research, analysed 23 isolates obtained from beef and pork samples purchased at retail outlets. After quality filtering, 18 high-quality whole genomes were retained. These were then placed alongside 356 publicly available food-associated genomes in a comparative framework, allowing the South African isolates to be situated within the global population structure of the species for the first time.

The methodological backbone of the study was core genome multilocus sequence typing, or cgMLST, a technique that compares the sequences of hundreds to thousands of genes shared by all strains in a species. By tallying the differences at these core loci, cgMLST produces a fine-grained measure of genetic relatedness that can reveal transmission chains, geographic clusters and evolutionary lineages with a resolution that older fingerprinting methods cannot match. In this analysis, the combined dataset resolved into four major lineages, and the South African isolates fell predominantly within a clade designated HC1490_10, a group that is widely distributed internationally.

Traditional multilocus sequence typing, which examines a smaller set of housekeeping genes and assigns each strain a sequence type or ST, added another layer of detail. The local isolates represented 11 distinct sequence types, including several that are potentially uncommon in the published literature: ST661, ST329, ST173 and ST352. At the same time, the researchers detected ST3, ST18 and ST178 among the South African samples, sequence types that belong to lineages known to be prevalent and widely distributed around the world. This mix of locally distinctive and globally shared types suggests that the meat supply carries both endemic diversity and strains with international connections.

Beyond relatedness, the team explored the pan-genome, the total complement of genes found across all strains of the species. Bacteria typically split their gene pool into a core of universally conserved genes and a vast accessory genome of genes present in only some strains. Yersinia enterocolitica showed what geneticists call an open pan-genome: as more genomes are added, new genes keep appearing, a pattern driven by a high proportion of accessory and so-called cloud genes, particularly in the global dataset. Open pan-genomes are signatures of substantial genomic plasticity, indicating that the species readily gains and loses DNA through horizontal gene transfer, the exchange of genetic material between organisms that reshapes bacterial populations over ecological timescales.

One of the most consequential questions for any foodborne pathogen survey is antimicrobial resistance. Here the study delivered a nuanced result. Profiling of the resistome, the full set of resistance-associated genes, revealed a conserved intrinsic resistome dominated by beta-lactamase genes, notably blaA and ampC, along with efflux-associated determinants that pump antibiotics out of the cell. These intrinsic genes are part of the species’ normal genetic makeup and are not typically associated with clinical treatment failure. By contrast, acquired resistance genes, which bacteria pick up from other organisms and which often confer clinically relevant drug resistance, were detected only at low frequencies, and intriguingly, they were confined to isolates belonging to the HC1490_10 clade.

The mobile genetic element analysis shed light on how this plasticity is achieved. The researchers identified a diverse array of plasmids, the small circular DNA molecules that bacteria exchange readily, and prophages, viral genomes integrated into the bacterial chromosome. Both play major roles in horizontal gene transfer and genome plasticity. Encouragingly, however, no plasmid-associated antimicrobial resistance genes were detected in the isolates studied, suggesting that the mobile elements circulating in these meat-associated populations are not currently ferrying clinically important resistance determinants between strains.

Virulence, not resistance, is the other half of the public health equation, and it was here that the study produced its most reassuring finding. The South African isolates lacked the plasmid-associated pathogenicity determinants that define dangerous strains, including the genes encoding the Type III secretion system, a molecular syringe that pathogenic yersiniae use to inject effector proteins into host cells and subvert the immune response. The local isolates were consequently classified as non-pathogenic biotype 1A. In stark contrast, the pathogenic lineage represented in the global dataset, designated HC1490_2, harboured both chromosomal and plasmid-encoded virulence factors, the full toolkit required to cause disease in humans.

These results place South African retail meat in a comparatively favourable light but come with important caveats. The dominance of non-pathogenic biotype 1A strains suggests a currently low virulence risk from the meat samples examined. Yet the presence of globally distributed lineages, including the clade in which acquired resistance genes were concentrated, underscores the potential for pathogenic variants to emerge or be introduced. Food production systems are dynamic, and the same open pan-genome that makes Yersinia enterocolitica so genomically flexible means that virulence and resistance traits can, in principle, move between lineages when conditions allow.

The authors argue that their findings make a direct case for integrating whole-genome sequencing into food safety and One Health surveillance frameworks, an approach that connects human, animal and environmental health into a single monitoring system. Genomic surveillance of this kind can trace contamination routes, flag the arrival of pathogenic clones, and detect emerging resistance before it becomes a clinical problem. For a country whose meat industry feeds millions and exports internationally, the message is clear: the bacteria on the supermarket shelf carry a genomic record of where they came from, and reading that record routinely could help keep one of food safety’s quieter threats from ever getting louder.

Subject of Research: Genomic epidemiology and antimicrobial resistance of Yersinia enterocolitica in South African meat and global populations

Article Title: Whole-genome sequencing reveals the genomic epidemiology of Yersinia enterocolitica in South African meat and global populations

Article References: Mashapo, M., Matle, I., Seakamela, E., & Mafuna, T. (2026). Whole-genome sequencing reveals the genomic epidemiology of Yersinia enterocolitica in South African meat and global populations. BMC Genomics. https://doi.org/10.1186/s12864-026-13409-z

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13409-z

Keywords: Yersinia enterocolitica, whole-genome sequencing, genomic epidemiology, antimicrobial resistance, virulence factors, pan-genome, cgMLST, food safety, meat contamination, South Africa, One Health, biotype 1A

Enterococci are gram-positive bacteria that normally colonize the intestinal tracts of humans and animals, where they usually live as harmless commensals. Yet two species in particular, Enterococcus faecalis and Enterococcus faecium, are among the most important causes of opportunistic and healthcare-associated infections. Enterococcus faecium is notorious for its capacity to acquire resistance to penicillins and, increasingly, to glycopeptides such as vancomycin, an antibiotic class introduced in 1955 that kills bacteria by binding to peptidoglycan precursors and blocking cell wall synthesis. Vancomycin-resistant enterococci were first described more than two decades after the drug’s introduction, and among resistant E. faecium isolates the vanB genotype has become the most prevalent in several European countries. VanB-type resistance is known for phenotypic variability, meaning that laboratory phenotype does not always reliably reflect the underlying resistance genes, a property that has now proven consequential in a dramatic way.

The public health stakes are considerable. The World Health Organization’s 2024 Bacterial Priority Pathogens List classifies vancomycin-resistant E. faecium as a high-priority pathogen, and according to the European Centre for Disease Prevention and Control the mean vancomycin resistance rate among European E. faecium isolates stands at roughly 20 percent. Austria had long reported comparatively low figures, with the national action program on antibiotic resistance documenting a resistance rate of just 3 percent among invasive isolates in 2023. That picture changed abruptly. After years without any invasive vancomycin-resistant E. faecium infections, the diagnostic laboratory serving Graz and the wider region observed the resistance rate among E. faecium-positive blood cultures climb to 6 percent in 2024 and then to 20 percent in the first half of 2025. By June 2025, thirty-one resistant isolates had been collected, and virtually all could be attributed to a single previously unreported lineage, ST117/CT7799.

The outbreak’s first signal appeared in February 2024, when automated VITEK2 susceptibility testing flagged vancomycin resistance in a clinical E. faecium isolate even though disk diffusion, gradient testing, and broth microdilution all failed to confirm it under routine conditions. When the laboratory reorganized its workflow to route all enterococcal isolates through automated testing and systematically re-examined results, five further isolates with the same distinctive phenotype emerged within months. All came from specimens obtained for genuine infection diagnostics rather than screening, and every case was confirmed as vanB-type resistance by molecular PCR. Retrospective review of raw instrument data found no evidence of this phenotype in the laboratory’s records before 2024, strongly suggesting a genuinely new arrival. Early cases clustered around invasive procedures performed at a single hospital, and a second transmission chain later surfaced among urology patients who had undergone double-J catheterization in an operating room shared with surgeons. Notably, environmental surface sampling by the hospital infection control team failed to locate the organism, and nearly all affected patients had either been hospitalized for at least four days or had recent inpatient care history with the same provider.

To characterize the outbreak, the team subjected twenty non-duplicate isolates to whole genome sequencing using both Illumina short-read and Oxford Nanopore long-read platforms, achieving highly concordant results between technologies. Core genome multilocus sequence typing based on 1,423 loci revealed a strikingly homogeneous cluster: even isolates sampled sixteen months apart differed by no more than six alleles, far below the cluster threshold of three alleles used for assignment once the clonal relationship was established. The nearest local control strain, isolated at the same site during the same period, differed by 159 alleles, and the closest reference strain from the Robert Koch Institute collection differed by 142 alleles. Searches of the cross-national surveillance platform MiGenomeSurv showed the next closest relative still 76 alleles away, confirming that CT7799 represents an entirely novel lineage. The clone was provisionally named VREfmstyr, after Styria, the Austrian federal state where it was first isolated.

Genomic analysis also illuminated the genetic architecture of resistance. All outbreak isolates carried a complete copy of the transposon Tn1549, the mobile element responsible for vanB-mediated vancomycin resistance, inserted into the chromosome. Long-read assemblies proved essential: short-read assemblies fragmented the transposon across three contigs, obscuring its structure, whereas long reads revealed three matching blocks separated by two intervening regions of 1,494 and 1,417 base pairs containing insertion sequence elements, including an ISL3-like transposase of the ISEfa11 family and an IS3-like ISEnfa3-family transposase alongside a helix-turn-helix domain protein. An additional IS91 transposase was found inserted in a YodL domain protein upstream of the vanB gene cluster. All seven vancomycin resistance genes, vanB, vanY-B, vanW-B, vanH-B, vanX-B, vanR-B, and vanS-B, were identical across every outbreak isolate, underscoring the clone’s remarkable genetic stability despite months of circulation. Based on the classification scheme of the Norwegian VRE study group, the vanB cassette appears to be a hybrid between variants typically associated with different sequence types, hinting at a recombination event in the strain’s recent history.

The true significance of the study, however, lies in its systematic evaluation of diagnostic methods, and the results are sobering. Broth microdilution, the reference standard for antimicrobial susceptibility testing, correctly identified only 16 of 31 isolates, or 52 percent, as vancomycin resistant when read after the standard 24 hours of incubation, even though all control strains behaved as expected. Extending incubation to 48 hours eventually pushed minimum inhibitory concentrations above the susceptibility breakpoint for all isolates, but the growth around concentrations of 2 milligrams per liter and above was so sparse that even trained personnel could easily overlook it. Gradient testing from two different manufacturers failed to detect resistance in every single case at 24 hours, and disk diffusion was equally deceptive: all isolates produced inhibition zone diameters clearly wider than the 12-millimeter resistance threshold, and the zone edges lacked the fuzzy appearance that typically signals vancomycin resistance. Only VITEK2 automated testing, which correctly flagged all 31 isolates under routine settings, proved reliable, a finding that diverges from earlier studies reporting only 81 percent sensitivity for low-MIC resistant strains and possibly reflecting improvements in newer test cards and software.

Screening carried a similar message of failure. When seven representative isolates were plated on kanamycin-vancomycin agar and four commercially available chromogenic VRE screening media, three of the four commercial agars yielded no growth at all after 24 hours, and the sole medium showing some activity was only weakly positive for four isolates and negative for the remaining three. Prolonging incubation to 48 and even 72 hours improved results only marginally and inconsistently across manufacturers, while the outbreak strain failed entirely to grow on kanamycin-vancomycin agar. These findings matter because VRE often constitutes only a small fraction of the intestinal enterococcal population, making selective screening media indispensable for controlling transmission, and because prior research has already shown that sensitivity drops sharply for strains with vancomycin minimum inhibitory concentrations below 16 milligrams per liter. Only CHROMagar VRE proved dependable after standard incubation, and even that required confirming results under the study’s specific conditions.

Intriguingly, when a representative isolate was exposed to vancomycin on a gradient strip for more than 100 hours, single colonies eventually grew within the inhibition zone, and after two passages the derivative consistently displayed a minimum inhibitory concentration of at least 32 milligrams per liter. Sequencing revealed that this resistant derivative carried a single nucleotide substitution in the vanS-B gene, the sensor kinase that regulates the vancomycin resistance operon, causing an amino acid change from serine to arginine at position 243. This observation suggests that the outbreak clone’s occult phenotype stems from a regulatory mutation or arrangement that dampens resistance expression, and that vancomycin pressure can select for compensatory variants restoring full resistance. The authors caution, however, that whether the insertion elements or the specific allele differences in vanR-B, vanY-B, and vanW-B are causally responsible for the difficult-to-detect phenotype remains an open question demanding further investigation.

The implications reach well beyond Styria. Because many diagnostic laboratories worldwide rely on 24-hour disk diffusion zone readings to determine vancomycin susceptibility, a strain with this phenotype could spread through hospitals without triggering any alarm, quietly colonizing patients and contaminating environments while appearing fully susceptible on paper. The research team recommends that laboratories verify the adequacy of their screening media and incubation times, and adapt their susceptibility testing protocols by prolonging incubation, adding molecular vanB PCR testing, or employing automated VITEK2 analysis. Given the clone’s demonstrated epidemic potential, its absence from all prior surveillance databases, and the growing proportion of invasive infections it now accounts for in the region, surveillance studies will be essential to determine whether ST117/CT7799 remains a local phenomenon or whether laboratories across Europe and beyond must urgently reassess whether their diagnostic procedures can catch a superbug designed, by evolutionary accident, to stay invisible.

Subject of Research: Emergence and diagnostic challenges of a novel vancomycin-resistant Enterococcus faecium clone (ST117/CT7799) in Austria

Article Title: Emergence of a Novel, Phenotypically Difficult‐to‐Detect Vancomycin‐Resistant Enterococcus faecium Clone (ST117/CT7799)

Article References: Forstner, P., Uitz, C., Dabernig‐Heinz, J., Wagner, G. E., Bender, J., Fischer, M., Siebenhofer, D., Werner, G., Busche, T., Klages, L. J., Rückert‐Reed, C., Steinmetz, I., & Dichtl, K. (2026). Emergence of a Novel, Phenotypically Difficult‐to‐Detect Vancomycin‐Resistant Enterococcus faecium Clone (ST117/CT7799). MicrobiologyOpen, 15(5), Article e70393. https://doi.org/10.1002/mbo3.70393

Image Credits: AI Generated

DOI: 10.1002/mbo3.70393

Keywords: vancomycin-resistant Enterococcus faecium, VRE, ST117/CT7799, hospital outbreak, antimicrobial resistance, vanB operon, Tn1549 transposon, whole genome sequencing, diagnostics, Austria, infection control, cgMLST