100 for 100: Shaping the Future of Antimicrobial Resistance Research

Item 84/100: The Worst of Both Worlds – Convergence of Antimicrobial Resistance and Hypervirulence in Klebsiella pneumoniae
James Budnick, PhD, Senior Scientist, Microbiology R&D
ATCC® 43816™ – Klebsiella pneumoniae subsp. pneumoniae (Schroeter) Trevisan

Klebsiella pneumoniae (first called Friedlander’s bacillus in the late 19th century) is ranked high as a current threat to human health by both the Centers for Disease Control and Prevention (CDC)¹ and World Health Organization (WHO).² This is due to this gram-negative bacterium’s ability to acquire resistance mechanisms—such as extended-spectrum beta-lactamase and carbapenemase encoding genes—that confer resistance to multiple antibiotics, making these infections very difficult to treat. “Classical Klebsiella” (cKp) are associated with hospital-acquired infections in patients with comorbidities and are more likely to become multidrug resistant.³ “Hypervirulent Klebsiella” (hvKp) represent another pathotype and are more commonly associated with community-acquired infections that are metastatic and more invasive in the human body as compared to an infection caused by cKp.⁴ While these infections have an increased chance of mortality, they are treatable as hvKp are generally susceptible to antibiotics.⁵ Current typing systems do not always accurately predict the distinction between classical and hypervirulent Klebsiella strains, which may be necessary to successfully treat these infections. Extensive genetic sequencing to characterize the core and accessory genomes has been promising in characterizing key differences between the two pathotypes.³

A nightmare scenario is starting to unfold as more genetic and epidemiological information is available on Klebsiella strains. These studies have highlighted the growing prevalence of convergent multidrug-resistant hypervirulent Klebsiella (MDR-hvKp) strains, which are both invasive and difficult to treat.⁶ This occurs when one pathotype acquires genetic elements from the other pathotype through mobile gene transfer. While many studies have focused on one pathotype acquiring mobile genetic elements from the other pathotype, there are reports of mosaic plasmids that contain genes of both pathotypes.³ This scenario highlights the growing need for increased understanding of both MDR and hypervirulent Klebsiella strains so that we are better prepared to combat them. To support this critical research area, ATCC offers a variety of Klebsiella pneumoniae strains that are widely used in research and clinical settings, including type strains (ATCC® 13883™)^7,8 hypervirulent strains for infection models (ATCC® 43816™), and numerous clinical isolates. Genetic information is crucial to furthering our understanding of this organism and fortunately, many of these strains have high-quality sequence information available in the ATCC Genome Portal.

Item 85/100: Antimicrobial-Resistant Strain from an Elementary School Outbreak
Meghan Sikes, MS, Senior Biologist
ATCC® BAA-946™ – Streptococcus pyogenes Rosenbach 

Most people have experienced strep throat or skin infections, like impetigo, as kids.  The common culprit of these mild infections is Streptococcus pyogenes, which can also cause serious infections like scarlet fever, necrotizing fasciitis (flesh-eating disease), or toxic shock syndrome.  This versatile gram-positive bacterium has a variety of virulence factors like a carbohydrate-based capsule, surface M protein, and exotoxin Streptolysin O⁹ that make it an extremely effective human pathogen. Since the COVID-19 pandemic, there have been drastic increases in invasive Streptococcus infections, especially in the United States.¹⁰ While S. pyogenes is usually treated with antibiotics, increasing resistance to a variety of antibiotics has allowed this pathogen to evade conventional treatments.  

S. pyogenes MGAS 10394 (ATCC® BAA-946™) is an erythromycin-resistant strain that was isolated from the throat culture of an elementary school student in Pittsburgh during a 2001 pharyngitis outbreak at a private school. Nearly 2000 throat cultures were collected from students, revealing an unusual emergence of erythromycin resistance.¹¹ This outbreak was found to be caused by a single erythromycin-resistant clone that was later deposited with ATCC in 2001 by JM Musser and J Martin.  Whole-genome sequencing of this strain identified the presence of the mefA gene, which encodes for a macrolide efflux protein.¹² As antimicrobial resistance continues to pose a growing public health threat, studying antibiotic resistant strains like S. pyogenes MGAS 10394 will become increasingly important for understanding resistance mechanisms and informing future treatment strategies.

Item 86/100: Turning Up the Heat!
Scott Nguyen, PhD, Senior Biocuration Scientist
ATCC® 43845™ – Salmonella enterica subsp. enterica (ex Kauffmann and Edwards) Le Minor and Popoff serovar Senftenberg

Salmonella enterica subsp. enterica serovar Senftenberg 775/W (ATCC® 43845™) has long served as a model organism for studying heat resistance in foodborne pathogens.¹³ This strain was first isolated in 1941 from dried egg powder by the Massachusetts Department of Public Health.¹⁴

By 1946, A.R. Winter had reported its heat resistance in liquid whole egg,¹⁵ and in 1969, Henry Ng highlighted its exceptional thermotolerance.¹⁶ As of 2025, over 1700 scientific publications in Google Scholar reference S. enterica subsp. enterica serovar Senftenberg 775/W for its heat and stress tolerance.

Despite decades of use in thermal inactivation studies, the genetic basis for this bacterium’s heat tolerance remained unknown until its full genome was sequenced in 2017.¹⁴ Researchers from the USDA Agricultural Research Service discovered that the strain harbors two transmissible loci of stress tolerance (tLST) on an IncHI2 plasmid .^14,17 Modern IncHI2 plasmids are known carriers of multiple antibiotic resistance genes in foodborne pathogens such as Salmonella and other Enterobacteriaceae.¹⁸ However, since S. enterica subsp. enterica serovar Senftenberg 775/W was isolated prior to common use of antibiotics, its stress tolerance traits like heat resistance may reflect the original genotypes of IncHI2 plasmids before widespread emergence of antibiotic resistance.^14,19

This strain has also been sequenced by the ATCC and the complete and closed genome is available in the ATCC Genome Portal. As a benchmark organism for heat resistance since the 1940s,  S. enterica subsp. enterica serovar Senftenberg 775/W continues to provide valuable insights into the evolution of IncHI2 plasmids and the acquisition of resistance determinants.

Item 87/100: Going Viral Against Bacteria: Phages Team Up to Fight Resistance
Sydney McKnight, MS, Biologist
ATCC® 11303-B4™ – Escherichia coli bacteriophage T4  

Antimicrobial resistance (AMR) is one of the greatest battles in modern medicine, with the Centers for Disease Control and Prevention (CDC) estimating over 2.8 million resistant infections in the U.S. each year.²⁰ As bacteria continue to adapt and evade treatment, researchers are forming a new kind of alliance by pairing antibiotics with bacteriophages—lytic viruses that specifically target and destroy bacteria without harming human cells.²¹ This partnership is known as phage–antibiotic synergy (PAS).

A leading example is Escherichia coli bacteriophage T4 (ATCC® 11303-B4™), which has become a model for studying PAS. In laboratory experiments, combining T4 with antibiotics such as cefotaxime increased phage activity—resulting in larger plaques, faster replication, and stronger bacterial clearance. Importantly, this combination was far more effective against E. coli biofilms than antibiotics alone.²²

Pairing phages with tobramycin has also shown remarkable promise. In both E. coli and Pseudomonas aeruginosa biofilms, the combination reduced the emergence of antibiotic-resistant and phage-resistant cells by over 99% and 39%, respectively, outperforming either treatment on its own.²³

The strength of PAS lies in a coordinated attack: antibiotics increase bacterial permeability and induce stress responses that favor phage activity, while phages break down protective biofilms to improve bacterial clearance.^24,25 Together, they form a strategic union that enhances bacterial killing and helps slow the development of resistance.

However, it’s not all universally positive, some phage-antibiotic pairings may yield indifferent or even antagonistic effects. The outcome depends heavily on factors like the specific phage, antibiotic, dose, timing, and bacterial strain involved.²⁶

In summary, E. coli bacteriophage T4 demonstrates how the combined force of phages and antibiotics can dismantle biofilms, improve bacterial clearance, and reduce resistance. Though most findings remain at the laboratory stage, PAS offers a promising alliance that could help bring a new hope for turning the tide in the ongoing fight against antimicrobial resistance.

Item 88/100: Firehammerviruses 
David Yarmosh, MS, Lead Bioinformatician
ATCC® 35922-B2™ – Campylobacter jejuni susp. jejuni bacteriophage 12

Campylobacter jejuni susp. jejuni bacteriophage 12—also known by its genus Firehammervirus—plays a substantial role in the poultry industry, particularly in the control of Campylobacter jejuni, a leading cause of foodborne illness globally.²⁷ C. jejuni is commonly found in the intestines of poultry, and while it typically does not harm the birds, it poses a significant health risk to humans through the consumption of contaminated meat. Firehammerviruses, a genus of lytic bacteriophages, specifically target and destroy C. jejuni, offering a promising biocontrol strategy to reduce bacterial loads in poultry before processing.

The significance of Firehammerviruses lies in their host specificity and lytic nature. Unlike antibiotics, which can disrupt the entire microbiome and contribute to resistance, these phages selectively infect C. jejuni without affecting beneficial bacteria. This precision makes them ideal for use in pre-harvest interventions, such as phage sprays or feed additives, to reduce contamination at the source. Studies have shown that phage treatment can significantly lower C. jejuni colonization in broiler chickens, which directly translates to safer poultry products and cleaner surfaces.²⁸

Moreover, Firehammerviruses possess unique genomic adaptations, such as the replacement of guanosine with the modified base 2’-deoxy-7-amido-7-deazaguanosine (dADG),²⁹ which helps them evade bacterial defense mechanisms. This makes them more resilient and effective in real-world agricultural environments, where bacterial resistance to phages can be a concern. Their robust nature enhances their potential as a sustainable alternative to antibiotics, aligning with global efforts to combat antimicrobial resistance in food production systems.

As regulatory frameworks evolve and consumer demand for antibiotic-free meat grows, Firehammerviruses could become a cornerstone of next-generation food safety practices. Their integration into poultry farming not only improves public health outcomes but also supports industry goals of sustainability and biosecurity. Continued research, next-generation sequencing, and field trials will be key to optimizing their application and ensuring consistent efficacy across diverse farming conditions.

Item 89/100: More Than Jewelry: The Effect of Gold on Antimicrobial-Resistant Bacteria
Katherine Morin, MS, Senior Biologist, Micro R&D 
ATCC® 51983™ – Klebsiella oxytoca (Flugge) Lautrop

In recent years, there has been an alarming increase in the number of infections caused by antimicrobial-resistant (AMR) pathogens, leading to serious health conditions and death worldwide. Approximately 40% of all reported AMR infections were caused by bacteria resistant to last-line antibiotics, making them nearly impossible to treat.³⁰ It is estimated that there will be a total of 300 million premature deaths and an economic cost of up to $100 trillion resulting from infections caused by multidrug-resistant (MDR) bacteria by the year 2050.³² Experts have found that nanoparticles are a promising alternative to traditional antimicrobials due to their ability to evade drug resistance mechanisms in bacteria, inhibit biofilm formation, and disrupt other processes related to a bacterium’s virulence potential.³¹

Gold nanoparticles (AuNPs) are attracting a lot of interest in the nanotechnology field.³¹ Bacterial cell membranes are negatively charged and create a physical barrier that restricts access to the membrane by many antimicrobial agents.³² AuNPs allow electrostatic interaction between the nanoparticles and the negatively charged membrane.³² AuNPs also aggregate inside the cell, disrupting protein efflux and ATPase pumps.³² This type of disruption leads to cell membrane damage, leading to bacterial cell death.³²

AuNPs can be supplemented with different substances to enhance antimicrobial effects. An in vitro study showed that the use of AuNPs modified with chitosan (Chi/AuNPs) had bactericidal effects against Klebsiella oxytoca H51574-2 (ATCC® 51983™), an extended spectrum beta-lactamase-producing bacterium that evades antimicrobial effects via inactivation of antibiotics through degrading enzymes.³³ The synergistic effects of the Chi/AuNPs on this organism caused disruption of bacterial membranes, making the organism incapable of avoiding the toxicity of the AuNPs. As K. oxytoca H51574-2 is a common antimicrobial-resistant strain and frequently used in AMR studies, including examining the antimicrobial effects of other types of metal-based nanoparticles like silver³³ and copper oxide,³⁴ this shows a positive and promising result for the development of alternative antimicrobials using nanotechnology to tackle the danger that is AMR.

Item 90/100: Advancing Biofilm Research with ATCC Strains
Jeanette Rimbey, MSc, Lead Biologist
ATCC® BAA-210™ – Pseudomonas aeruginosa (Schroeter) Migula

Biofilms are structured communities of bacteria encased in a self-produced matrix that pose significant challenges across healthcare, industry, and environmental systems. Their remarkable resilience against antibiotics and disinfectants has made them a central focus of microbiological research. Pseudomonas aeruginosa PA14 (ATCC® BAA-210™) is a key strain in biofilm research due to its aggressive colonization behavior and unique biofilm formation mechanisms, making it especially valuable for studying biofilm invasion, virulence, and environmental adaptability.  P. aeruginosa PA14 has been a cornerstone of microbiological research since 1977. Known for its high virulence and robust biofilm formation, PA14’s genetic versatility and environmental adaptability make it an ideal model for studying quorum sensing, antibiotic resistance, and biofilm dynamics. Research using authenticated ATCC strains like PA14 drives innovation in anti-biofilm strategies, from novel antimicrobials and medical device coatings to sanitation practices, ensuring reproducible and high-impact results across disciplines.

Item 91/100: Colistin, the Last Line of Defense
Scott Nguyen, PhD, Senior Biocuration Scientist
ATCC® 842™ – Paenibacillus polymyxa (Prazmowski) Ash et al.

Colistin, also known as polymyxin E, is a critical antibiotic used as a last resort against multidrug-resistant gram-negative bacteria.³⁵ Despite its importance in human medicine, colistin has been widely used in veterinary medicine for the last few decades.³⁶ This widespread use has contributed to the emergence of resistance, most notably with the discovery of the horizontally acquired mcr-1 gene in 2016.³⁷

Colistin is produced by Paenibacillus polymyxa and one of the most studied P. polymyxa strains is Paenibacillus E681.³⁸ The biosynthetic gene cluster responsible for colistin production in strain E681 was sequenced and deposited under NCBI accession EU371992.³⁹ Characterization of this biosynthetic gene cluster shows it produces a mixture of polymyxin E1 and E2.⁴⁰

Recent genomic mining efforts have expanded our understanding of colistin biosynthesis. Chen et al. reported that P. polymyxa ATCC® 842™,⁴¹ the type strain of P. polymyxa, is a natural producer of colistin. Comparative analysis shows that all sequenced P. polymyxa in the ATCC Genome Portal possess related, but not identical biosynthetic gene clusters as compared to E681 (Figure 1). These findings suggest a broader diversity in colistin biosynthesis pathways than previously recognized and may offer novel solutions to colistin resistance.

Figure 1: The polymyxin biosynthetic gene cluster (Pmx BGC) from Paenibacillus polymyxa E681 (GenBank: EU371992) was used as a reference in a BLAST analysis to identify related BGCs in sequenced P. polymyxa strains from the ATCC Genome Portal (ATCC® 15970™, ATCC® 842™, ATCC® 43865™, and ATCC® 7070™). The Pmx BGC genes (pmxA, pmxB, pmxC, pmxD, and pmxE) are color-coded (purple, green, orange, red, and blue, respectively). A greyscale identity bar below the BLAST analysis indicates nucleotide similarity, with darker shades representing higher identity. The analysis reveals that while the Pmx BGCs are highly conserved, they exhibit sufficient sequence diversity to suggest potential structural variation in the encoded polymyxin compounds. This diversity may offer avenues to overcome emerging colistin resistance.

Did you know?

Antimicrobial resistance remains dangerously underestimated by the public. In 2019 alone, antibiotic-resistant infections claimed more lives in the U.S. than two-thirds of the total American military fatalities during the entire Vietnam War.⁴²

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