Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method
Abstract Background Even with state-of-the-art infection control practices, premature infants can develop life-threatening infections in the neonatal intensive care unit (NICU). The precise sources of most NICU-associated infections frequently remain unknown and, therefore, are difficult to address....
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| Language: | English |
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BMC
2025-07-01
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| Series: | Antimicrobial Resistance and Infection Control |
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| Online Access: | https://doi.org/10.1186/s13756-025-01609-3 |
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| author | Adam P. Matson Katrin Unterhauser Karim Rezaul Stephanie Lesmes Yanjiao Zhou Ian C. Michelow Naveed Hussain Mark D. Driscoll |
| author_facet | Adam P. Matson Katrin Unterhauser Karim Rezaul Stephanie Lesmes Yanjiao Zhou Ian C. Michelow Naveed Hussain Mark D. Driscoll |
| author_sort | Adam P. Matson |
| collection | DOAJ |
| description | Abstract Background Even with state-of-the-art infection control practices, premature infants can develop life-threatening infections in the neonatal intensive care unit (NICU). The precise sources of most NICU-associated infections frequently remain unknown and, therefore, are difficult to address. In this study, we used a novel microbiome sequencing approach to source-track lethal sepsis-causing Klebsiella, opportunistic pathogens, and commensal bacterial strains colonizing the gut of hospitalized premature infants. Methods An exploratory-methods, case series was at performed Connecticut Children’s Medical Center NICU in 2021. Long-read 16–23 S rRNA gene sequencing was used to analyze fecal samples, mother’s milk, and clinical bacterial isolates derived from a cluster of Klebsiella-infected, and concurrently hospitalized non-infected, premature infants who were simultaneously enrolled in a neonatal microbiome study. Distinct groups of amplicons comprising a unique fingerprint pattern for a given strain were compared among the samples to ascertain relatedness. Results We confirmed 100% amplicon identity between lethal Klebsiella quasipneumoniae from milk, gut, blood and trachea during sepsis in twins, while differentiating other infecting and colonizing Klebsiella strains in concurrently hospitalized premature infants. The method also successfully discriminated between multiple Klebsiella strains within the gut microbiota of a non-infected infant. Additionally, we showed that human milk is the source of many early intestinal colonizers, including Klebsiella, Enterococcus, Veillonella, and Bifidobacterium strains. Conclusions Amplicon fingerprinting can be utilized as a high-throughput high-resolution test to assist in the investigation of nosocomial outbreaks. Additional applications such as routine monitoring of various reservoirs for potential pathogens could inform infection prevention and control strategies in the NICU. |
| format | Article |
| id | doaj-art-7f100c7349634c72bbb0b3570e6a5d47 |
| institution | Kabale University |
| issn | 2047-2994 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Antimicrobial Resistance and Infection Control |
| spelling | doaj-art-7f100c7349634c72bbb0b3570e6a5d472025-08-20T03:41:57ZengBMCAntimicrobial Resistance and Infection Control2047-29942025-07-011411810.1186/s13756-025-01609-3Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting methodAdam P. Matson0Katrin Unterhauser1Karim Rezaul2Stephanie Lesmes3Yanjiao Zhou4Ian C. Michelow5Naveed Hussain6Mark D. Driscoll7Department of Pediatrics, UConn HealthDepartment of Pediatrics, UConn HealthDepartment of Pediatrics, UConn HealthDepartment of Research, Connecticut Children’s Medical CenterDepartment of Medicine, UConn HealthDepartment of Pediatrics, UConn HealthDepartment of Pediatrics, UConn HealthIntus BiosciencesAbstract Background Even with state-of-the-art infection control practices, premature infants can develop life-threatening infections in the neonatal intensive care unit (NICU). The precise sources of most NICU-associated infections frequently remain unknown and, therefore, are difficult to address. In this study, we used a novel microbiome sequencing approach to source-track lethal sepsis-causing Klebsiella, opportunistic pathogens, and commensal bacterial strains colonizing the gut of hospitalized premature infants. Methods An exploratory-methods, case series was at performed Connecticut Children’s Medical Center NICU in 2021. Long-read 16–23 S rRNA gene sequencing was used to analyze fecal samples, mother’s milk, and clinical bacterial isolates derived from a cluster of Klebsiella-infected, and concurrently hospitalized non-infected, premature infants who were simultaneously enrolled in a neonatal microbiome study. Distinct groups of amplicons comprising a unique fingerprint pattern for a given strain were compared among the samples to ascertain relatedness. Results We confirmed 100% amplicon identity between lethal Klebsiella quasipneumoniae from milk, gut, blood and trachea during sepsis in twins, while differentiating other infecting and colonizing Klebsiella strains in concurrently hospitalized premature infants. The method also successfully discriminated between multiple Klebsiella strains within the gut microbiota of a non-infected infant. Additionally, we showed that human milk is the source of many early intestinal colonizers, including Klebsiella, Enterococcus, Veillonella, and Bifidobacterium strains. Conclusions Amplicon fingerprinting can be utilized as a high-throughput high-resolution test to assist in the investigation of nosocomial outbreaks. Additional applications such as routine monitoring of various reservoirs for potential pathogens could inform infection prevention and control strategies in the NICU.https://doi.org/10.1186/s13756-025-01609-3KlebsiellaMicrobiomeSource-trackingNeonatal infectionsLong-read sequencing16S rRNA |
| spellingShingle | Adam P. Matson Katrin Unterhauser Karim Rezaul Stephanie Lesmes Yanjiao Zhou Ian C. Michelow Naveed Hussain Mark D. Driscoll Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method Antimicrobial Resistance and Infection Control Klebsiella Microbiome Source-tracking Neonatal infections Long-read sequencing 16S rRNA |
| title | Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method |
| title_full | Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method |
| title_fullStr | Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method |
| title_full_unstemmed | Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method |
| title_short | Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method |
| title_sort | source tracking klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method |
| topic | Klebsiella Microbiome Source-tracking Neonatal infections Long-read sequencing 16S rRNA |
| url | https://doi.org/10.1186/s13756-025-01609-3 |
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