Antimicrobial resistance in poultry: broiler carcass study

Antimicrobial resistance in poultry is already a present-day problem, not a distant one. A study of 60 Brazilian broiler carcasses found multidrug-resistant Salmonella, Escherichia coli, and ESKAPE pathogens carrying clinically relevant resistance genes. Genomic analysis linked several isolates to human infection strains, showing poultry can act as a reservoir for bacteria that threaten human treatment. The findings point to gaps in current surveillance.

Why antimicrobial resistance in poultry matters for food safety

Brazil is the world’s largest chicken meat exporter, and global production reached 128 million tons in 2024, overtaking pork as the most produced meat. Poultry now supplies the largest share of animal protein consumed worldwide, with forecasts putting it at 45 percent of all meat protein by 2034. That scale makes antimicrobial resistance in poultry a direct public health lever, because poultry carries multidrug-resistant bacteria across borders at enormous volume.

Foodborne disease already causes about 600 million illnesses and 420,000 deaths each year. The bacteria behind many of those cases are becoming harder to treat. The World Health Organization lists antimicrobial resistance as a major threat and has published a priority pathogen list that includes the ESKAPE group and extended-spectrum beta-lactamase producing Enterobacterales. Poultry sits at the center of that risk because it moves from farm to fork at high volume and across many countries.

What the study looked at

Researchers sampled 60 broiler carcasses at a federally inspected slaughterhouse near Belo Horizonte, Brazil, that supplies both domestic and export markets. Half the carcasses showed visible gastrointestinal contamination and half did not. Sampling ran over six consecutive weeks, ten carcasses per week. From each carcass they isolated up to three colonies and identified them with MALDI-TOF mass spectrometry.

Susceptibility testing followed CLSI veterinary standards using disk diffusion. Isolates resistant to three or more antimicrobial classes were called multidrug-resistant. Extended-spectrum beta-lactamase production was confirmed with a double-disk synergy test, and AmpC beta-lactamase with a cefoxitin-cloxacillin variant. Twelve multidrug-resistant isolates were taken for whole-genome sequencing on an Illumina platform, with resistance genes called by ResFinder and plasmids by PlasmidFinder.

Parameter	Detail
Sample size	60 broiler carcasses, 30 with visible gut contamination and 30 without
Source	One federally inspected slaughterhouse near Belo Horizonte, Brazil
Sampling window	Six consecutive weeks, ten carcasses per week
Susceptibility method	CLSI VET01-Ed6 disk diffusion; CLSI M100-Ed31 breakpoints
MDR definition	Resistance to three or more antimicrobial classes
ESBL test	Ceftriaxone plus amoxicillin-clavulanate double-disk synergy
AmpC test	Cefoxitin-cloxacillin double-disk synergy
Sequencing	Illumina MiSeq 2 x 250 bp; SPAdes assembly; ResFinder 4.7.2; PlasmidFinder 2.0.1; MLST
Genomes sequenced	12 multidrug-resistant isolates, 4 Salmonella Minnesota, 5 E. coli, 3 Klebsiella pneumoniae

How widespread was resistance

The study recovered 48 Salmonella isolates, 99 E. coli, and a full ESKAPE panel. The resistance rates were high across the board.

Pathogen (isolates)	Resistant to at least one drug	Multidrug-resistant	ESBL-producing
Salmonella spp. (48)	52.1 percent	100 percent of resistant	52.1 percent
E. coli (99)	98 percent	84.8 percent	56.6 percent
Klebsiella pneumoniae (68)	100 percent	47.1 percent	13.2 percent
Enterobacter spp. (53)	100 percent	83 percent	not reported
Pseudomonas aeruginosa (59)	8 strains	0 percent	not applicable
Acinetobacter baumannii (14)	6 strains	2 strains	not applicable
Staphylococcus aureus (10)	5 strains MDR	5 strains	no MRSA found

Salmonella Minnesota dominated the resistant isolates

Among the 48 Salmonella isolates, 52.1 percent were resistant to at least one drug and every one of those was multidrug-resistant. More than half resisted third-generation cephalosporins, tetracyclines, and penicillins. The striking part is serotype: 24 of the 25 multidrug-resistant Salmonella were Salmonella Minnesota, or 96 percent. The association between that serotype and the resistant phenotype was enormous, with an odds ratio of 767.7.

E. coli carried ESBL at 56.6 percent

E. coli was nearly universal in its resistance. Ninety-eight percent resisted at least one antimicrobial and 84.8 percent were multidrug-resistant. Most telling, 56.6 percent produced extended-spectrum beta-lactamases, a rate the authors note is higher than comparable carcass studies in Africa and Asia. High resistance also appeared for penicillins at 82.8 percent, first-generation cephalosporins at 75.8 percent, and aminoglycosides at 71.7 percent.

The ESKAPE picture

All ESKAPE members turned up except Enterococcus faecium. Klebsiella pneumoniae showed 100 percent resistance to at least one drug and 47.1 percent multidrug resistance, with fluoroquinolone resistance strongly tied to the multidrug phenotype, odds ratio 13. Enterobacter spp. were 83 percent multidrug-resistant. Pseudomonas aeruginosa and Acinetobacter baumannii showed lower multidrug rates, and Staphylococcus aureus isolates were methicillin susceptible but five carried inducible clindamycin resistance.

The genomic red flags

Whole-genome sequencing is where the study becomes a human health story. The beta-lactamase genes found here disable front-line antibiotics used in both animal and human medicine. All four Salmonella Minnesota isolates belonged to sequence type ST548, a lineage tied to this serotype in Brazilian poultry. Within the study they differed by only 1 to 31 single nucleotide polymorphisms, but their resistance gene cargo was consistent: every sequenced strain carried genes for aminoglycoside, folate, and tetracycline resistance plus the AmpC gene blaCMY-2 and the plasmid-mediated quinolone resistance gene qnrB19.

The study shows antimicrobial resistance in poultry is tightly linked to strains from human clinics, not just farm animals. First, the Salmonella strains sat close to human infection isolates. The nearest human-derived genome, a Brazilian case, differed by only 33 single nucleotide polymorphisms, with others from the United Kingdom and Australia within 37 to 51. Second, the E. coli and Klebsiella pneumoniae isolates included internationally disseminated high-risk clones: E. coli ST38 and Klebsiella pneumoniae ST307. Strain 636 of ST307 carried a multi-replicon plasmid, and two Klebsiella strains carried an IncFIB plasmid associated with the carbapenem resistance gene blaNDM-1.

The counterintuitive part

The most uncomfortable result is a surveillance blind spot. Brazil requires slaughterhouses to monitor Salmonella in carcasses, but only for five serovars: Enteritidis, Typhimurium, Gallinarum, Pullorum, and monophasic Typhimurium. Salmonella Minnesota is not on that list. Yet in this study it was the dominant resistant serotype, accounting for 96 percent of multidrug-resistant Salmonella and carrying both ESBL and AmpC machinery.

That gap matters because the bacteria are not staying in the plant. The genomic trees show chicken isolates clustering near strains from human infections and from the very countries that import Brazilian chicken, including China. A recent study cited by the authors documented multidrug-resistant Salmonella Minnesota moving from Brazil into China through imported meat. International trade, in other words, can circulate successful resistant lineages as efficiently as local production creates them.

What producers and regulators can do

• Expand routine poultry surveillance beyond the current five serovars so emerging threats like Salmonella Minnesota are caught early.
• Tighten carcass decontamination and processing hygiene at the evisceration step, where visible gut contamination drives isolate recovery.
• Track plasmid-borne resistance genes, not just bacterial species, because blaCMY-2, blaCTX-M, and blaNDM-1 travel on mobile elements.
• Coordinate surveillance across export markets so a clone found in one country is traced through the supply chain.
• Reduce unnecessary antimicrobial use in flocks, since selective pressure sustains the multidrug phenotypes seen here.

Limitations of the study

This was a preliminary screen from a single slaughterhouse with 60 carcasses, so the numbers should not be read as national prevalence. Isolates from the same carcass may be clonally related, and the statistical tests treated each isolate as independent, which can inflate association strength. Plasmid structures were reconstructed from short-read data, which cannot always resolve complete plasmids, so the exact genetic context of some resistance genes remains uncertain. The authors also state nine isolates were sequenced in the methods yet describe twelve in the results, a discrepancy worth resolving in follow-up work. Larger multi-plant studies across Brazilian regions are needed.

Bottom line

Antimicrobial resistance in poultry is not a future worry but a present one. This Brazilian slaughterhouse study shows broiler carcasses carrying multidrug-resistant Salmonella, E. coli, and ESKAPE pathogens whose genomes link them to human infections, including globally disseminated high-risk clones. The fact that the dominant resistant serotype sits outside current monitoring rules is the clearest signal that surveillance needs to catch up.

FAQ

What is antimicrobial resistance in poultry

Antimicrobial resistance in poultry means bacteria carried by chickens and their meat can no longer be killed by drugs that once worked. In this study, 98 percent of E. coli and all Klebsiella pneumoniae isolates from broiler carcasses resisted at least one drug, and many resisted several classes at once. The resistance is concerning because some of these bacteria also cause human illness.

How common is ESBL-producing E. coli in Brazilian chicken

In the sampled carcasses, 56.6 percent of E. coli isolates produced extended-spectrum beta-lactamases, enzymes that defeat third-generation cephalosporins used in human medicine. That figure was higher than comparable carcass studies in Africa and Asia. The authors recovered 99 E. coli isolates, and 84.8 percent were multidrug-resistant overall.

Why does Salmonella Minnesota matter in broiler carcasses

Salmonella Minnesota was the dominant serotype among resistant isolates, making up 96 percent of multidrug-resistant Salmonella in the study. All four sequenced strains belonged to sequence type ST548 and carried both ESBL and AmpC resistance genes. Its absence from Brazil’s mandatory surveillance list means this threat can spread unnoticed through the poultry chain.

What are ESKAPE pathogens in food safety

ESKAPE stands for Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These bacteria are flagged by the World Health Organization as top priority threats because they acquire resistance easily. This study found every ESKAPE member except E. faecium on Brazilian broiler carcasses.

Which resistance genes were found on Brazilian chicken

The sequenced isolates carried genes for aminoglycoside, folate, and tetracycline resistance plus blaCMY-2, an AmpC beta-lactamase gene, and qnrB19, a plasmid-mediated quinolone resistance gene. E. coli also carried blaCTX-M variants. Two Klebsiella strains carried an IncFIB plasmid linked to blaNDM-1, a carbapenem resistance gene of last-resort concern.

How are chicken bacteria linked to human infections

Genomic comparison showed the carcass Salmonella strains sat within 33 to 51 single nucleotide polymorphisms of human infection isolates from Brazil, the United Kingdom, and Australia. E. coli ST38 and Klebsiella pneumoniae ST307 found on chicken are also known human high-risk clones. The close genetic distance suggests foodborne transmission is plausible rather than hypothetical.

What is the difference between ESBL and AmpC beta-lactamases

Both are enzymes that break down beta-lactam antibiotics, but they differ in scope and inhibition. ESBLs defeat third-generation cephalosporins and are blocked by clavulanate. AmpC enzymes resist cephamycins and are not inhibited by clavulanate, making them harder to manage. In this study, 52.1 percent of Salmonella were both ESBL and AmpC positive at once.

Why is Klebsiella pneumoniae ST307 a concern

ST307 is a globally disseminated, multidrug-resistant Klebsiella pneumoniae clone with established clinical importance. The study found it on a Brazilian broiler carcass, and the strain carried a multi-replicon plasmid associated with ESBL and carbapenemase spread. Its presence in food signals a potential bridge from farms to human healthcare settings.

Does Brazil monitor Salmonella Minnesota in poultry

No. Brazil requires slaughterhouses to test carcasses for only five Salmonella serovars: Enteritidis, Typhimurium, Gallinarum, Pullorum, and monophasic Typhimurium. Salmonella Minnesota is excluded. This study argues that exclusion is a gap, because Minnesota was the predominant resistant serotype and carried clinically relevant resistance genes.

What can poultry producers do to reduce antimicrobial resistance

Producers can tighten evisceration hygiene to cut gut contamination, expand serotyping beyond the five mandated serovars, and track plasmid-borne resistance genes. Coordinated surveillance with import markets helps trace clones through trade. Reducing unnecessary flock antimicrobial use lowers the selective pressure that sustains multidrug-resistant phenotypes in the first place.

How reliable are these broiler carcass findings

The results come from a single federally inspected slaughterhouse with 60 carcasses, so they are a preliminary screen, not national prevalence. Isolates from one carcass may be clonal, and short-read sequencing cannot fully resolve plasmid structures. The authors frame the work as an initial assessment that needs confirmation across more plants and regions.

What does this mean for consumers buying chicken

Consumers should treat raw chicken as a potential carrier of drug-resistant bacteria and follow basic handling rules: separate raw meat from other foods, cook to a safe internal temperature, and wash hands and surfaces after contact. The study does not measure risk per serving, but it shows resistant pathogens are present in the supply chain and warrant normal food safety practice.