Background Antibiotic resistance (AR) is an imminent threat to developing nations where poor sanitation and untreated wastewater remain major risk factors. In this study, Cuttack’s raw municipal sewage effluent (RMSE) was leveraged to investigate the potential escape of carbapenem-resistant Klebsiella pneumoniae (CRKP) into the environment and its prevalence in the urban population. Their genetic relatedness with clinical CRKP isolates was evaluated using repetitive element sequence-based PCR (rep-PCR) and (GTG)5-PCR. Results Eleven (n = 11) CRKP isolates, exhibiting variable resistance to 15 antibiotic classes, were recovered from RMSE. These isolates harboured several clinically relevant carbapenemase genes, including blaKPC (18.18%), blaIMP (18.18%), blaNDM (9.09%) with blaVIM (54.54%) and blaOXA-48-like (54.54%) being the most prevalent. In contrast, the clinical CRKP isolates (n = 14) were predominantly characterized by blaNDM (78.5%). The co-carriage of blaVIM + blaOXA-48-like was the most frequent combination in RMSE-derived isolates (45.45%), while clinical isolates were dominated by blaNDM + blaOXA-48-like (42.85%). Notably, many clinical isolates were marked by the confluence of extensively drug-resistant (XDR) (50%) phenotype and hypervirulent markers including iucA, iroB, rmpA, rmpA2 and peg-344. The clinical and environmental CRKP isolates clustered into two separate clades and differed significantly in their Multiple Antibiotic Resistance (MAR) Index (p < 0.00078), Minimum Inhibitory Concentration (MIC) of meropenem (p < 0.028) and imipenem (p < 0.019), number of β-lactamase genes (p < 0.0022), siderophore genes (p < 0.00039), and porin genes (p < 0.0001), as determined by the Mann–Whitney U-test. An XDR strain of the international high-risk clone ST395 harbouring a chromosomally encoded blaNDM-5 gene was also recovered from the RMSE. Conclusion These findings underscore the need for tailored strategies to mitigate community-associated and hospital-acquired CRKP infections, respectively, while identifying Cuttack’s RMSE as an escape gate for CRKP into the environment. The alarming presence of this superbug in RMSE further reflects its prevalence and ongoing cryptic transmission in Cuttack’s urban population. Our study advocates for the integration of sewage surveillance as a robust, cost-effective approach to monitor the environmental spread and current trends of pathogens in human populations. Graphical Abstract

Environmental trafficking of superbug carbapenem-resistant Klebsiella pneumoniae and its silent spread in an urban population: a sewage-based study

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2025年7月30日

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Saubhagini Sahoo,
Anshuman Sahu,
Rajesh Kumar Sahoo,
Mahendra Gaur,
Debadutta Bhanjadeo,
Enketeswara Subudhi

摘要

Background

Antibiotic resistance (AR) is an imminent threat to developing nations where poor sanitation and untreated wastewater remain major risk factors. In this study, Cuttack’s raw municipal sewage effluent (RMSE) was leveraged to investigate the potential escape of carbapenem-resistant Klebsiella pneumoniae (CRKP) into the environment and its prevalence in the urban population. Their genetic relatedness with clinical CRKP isolates was evaluated using repetitive element sequence-based PCR (rep-PCR) and (GTG)₅-PCR.

Results

Eleven (n = 11) CRKP isolates, exhibiting variable resistance to 15 antibiotic classes, were recovered from RMSE. These isolates harboured several clinically relevant carbapenemase genes, including bla_KPC (18.18%), bla_IMP (18.18%), bla_NDM (9.09%) with bla_VIM (54.54%) and bla_OXA-48-like (54.54%) being the most prevalent. In contrast, the clinical CRKP isolates (n = 14) were predominantly characterized by bla_NDM (78.5%). The co-carriage of bla_VIM + bla_OXA-48-like was the most frequent combination in RMSE-derived isolates (45.45%), while clinical isolates were dominated by bla_NDM + bla_OXA-48-like (42.85%). Notably, many clinical isolates were marked by the confluence of extensively drug-resistant (XDR) (50%) phenotype and hypervirulent markers including iucA, iroB, rmpA, rmpA2 and peg-344. The clinical and environmental CRKP isolates clustered into two separate clades and differed significantly in their Multiple Antibiotic Resistance (MAR) Index (p < 0.00078), Minimum Inhibitory Concentration (MIC) of meropenem (p < 0.028) and imipenem (p < 0.019), number of β-lactamase genes (p < 0.0022), siderophore genes (p < 0.00039), and porin genes (p < 0.0001), as determined by the Mann–Whitney U-test. An XDR strain of the international high-risk clone ST395 harbouring a chromosomally encoded bla_NDM-5 gene was also recovered from the RMSE.

Conclusion

These findings underscore the need for tailored strategies to mitigate community-associated and hospital-acquired CRKP infections, respectively, while identifying Cuttack’s RMSE as an escape gate for CRKP into the environment. The alarming presence of this superbug in RMSE further reflects its prevalence and ongoing cryptic transmission in Cuttack’s urban population. Our study advocates for the integration of sewage surveillance as a robust, cost-effective approach to monitor the environmental spread and current trends of pathogens in human populations.

Graphical Abstract